ARMY VETERAN WILLIAM PENNER used to jokingly call the thick yellow crust that crept across his young son Matthew’s scalp “Agent Orange” after the toxic defoliant sprayed on him in Vietnam before the boy was born. The joke turned sour a few years ago, when Matthew, now 43, was diagnosed with a host of serious illnesses, including heart disease, fibromyalgia and arthritis.

They, like thousands of others, are grappling with a chilling prospect: Could Agent Orange, the herbicide linked to health problems in Vietnam veterans, have also harmed their children?

For decades, the Department of Veterans Affairs has collected — and ignored — reams of information that could have helped answer that question, an investigation by ProPublica and The Virginian-Pilot has found.

Its medical staff has physically examined more than 668,000 Vietnam veterans possibly exposed to Agent Orange, documenting health conditions and noting when and where they served. For at least 34 years, the agency also has asked questions about their children’s birth defects, before and after the war.

But the birth defect data had never received scrutiny by the VA or anyone else until this year, when ProPublica, working with The Virginian-Pilot, obtained it after submitting a detailed plan describing how it would be used and agreeing to protect patients’ identities.

The analysis that followed was revealing: The odds of having a child born with birth defects during or after the war were more than a third higher for veterans who say they handled, sprayed or were directly sprayed with Agent Orange than for veterans who say they weren’t exposed or weren’t sure. The analysis controlled for such variables as age and health status.

The data has some caveats. The VA, for example, had no way of verifying the vets’ Agent Orange exposure and did not independently confirm information about their children’s birth defects. Even so, experts said the results should prompt the VA to take the issue seriously.

“It’s like a sign that says ‘Dig Here’ and they’re not digging,” said Dr. David Ozonoff, a professor of environmental health at Boston University and co-editor-in-chief of the online journal Environmental Health, after reviewing ProPublica’s findings. “It raises questions about whether they want to know the answer or are just hoping the problem will naturally go away as the veterans die off.”

Joel Michalek, co-author of a major Air Force study into Agent Orange exposure and birth defects, said ProPublica’s analysis suggests the issue should be revisited. In the 1980s, he and his team found a higher rate of post-war birth defects in the children of veterans who handled Agent Orange than in the children of those who didn’t, but they later concluded that herbicide exposure was not the cause.

“You see parallel patterns of what we saw back then,” said Michalek, a professor of epidemiology and biostatistics at the University of Texas Health Science Center at San Antonio. “That, to me, is a signal.”

In a written response on Thursday, the VA called ProPublica’s findings “interesting” and “a step in the right direction,” saying they raise additional questions.

But the agency also said it does not have the in-house expertise to study birth defects, deferring to academic researchers and other parts of the federal government. “VA believes that research to understand the relationship between exposure and intergenerational transmission of disease, if conducted, should be done where scientists with expertise in the relevant fields of inquiry can provide leadership.”

The VA said it should play “an ancillary role.”

Concerns that Agent Orange was not just sickening vets but also causing birth defects in their children surfaced after troops returned from war four decades ago. Veterans reported that some of their children had unusual defects — missing limbs, extra limbs and other diseases — that didn’t run in their families. Some government studies were done, including Michalek’s, but they generally dismissed an association.

Since then, those findings have guided the government position on disability benefits for children of Vietnam vets. The VA makes payments only to those who have spina bifida, in which the spinal cord doesn’t develop properly, and the children of a small number of female Vietnam vets with 18 other diseases. That leaves out the vast majority of vets’ ailing children.

Last week, after repeated recommendations by federal scientific advisory panels, Congress passed a bill that requires the VA to pay for an analysis of all research done thus far on the “descendents of veterans with toxic exposure.” It also requires the agency to determine the feasibility of future research and, if such studies are possible, to pursue them.

In its written response, the VA said it has already requested a related report from the National Academy of Medicine.

Recent advances in science, especially in the burgeoning field of epigenetics, have shown that chemical exposure can affect multiple generations. Changes in gene expression — whether a gene for a trait is turned on or off — can be passed from one generation to the next, research shows. A 2012 study, for example, showed that gestating female rats exposed to dioxin, a byproduct found in Agent Orange, passed mutations to future generations.

“I think there’s kind of a paradigm shift that’s been going on,” said Linda Birnbaum, director of the National Institute for Environmental Health Sciences, part of the National Institutes of Health. “While I used to be pretty skeptical about reports, especially related to Agent Orange exposures of predominantly male soldiers we had at the time, I’m not as skeptical as I was.”

If researchers conclude that troops’ wartime exposures can affect future generations, the implications go well beyond Vietnam veterans and their descendants. Vets from subsequent conflicts have similar concerns that their proximity to burn pits, depleted uranium and other toxins might be affecting their children.

Vietnam vets and their advocates believe a brutal calculation may lie at the heart of why their claims have gone unexamined. Caring for and compensating veterans themselves already costs tens of billions of dollars a year. If a link to their children is proven, it could add billions more.

Many Vietnam veterans, reaching the ends of their lives, are increasingly haunted by thoughts of the full cost of their service.

Blackledge, who fathered a healthy child before the war and two sick ones after, believes the government that exposed troops to Agent Orange should care for those it harmed — including their children.

“I probably wouldn’t have had kids,” he said, “had I known that there would be an impact on them.”

MIKE RYAN, AN ARMY VET, recalled seeing planes spraying Agent Orange overhead during his 13-month Vietnam tour but thought little of it until 1976, when his wife, Maureen, made the connection between the toxic herbicide and their daughter, Kerry.

From 1962 to 1971, the U.S. military sprayed millions of gallons of potent weed killers, including Agent Orange, over Vietnam to kill dense jungle foliage and eliminate places for the enemy to hide, exposing as many as 2.6 million service members in the process.

Many, like Ryan, returned home, eager to put Vietnam behind them, starting new families or adding to ones they had. Kerry was born in 1971 with a hole in her heart, no lower digestive system, dysfunctional kidneys, a deformed arm and fingers, spina bifida and more than a dozen other health problems.

Mike Ryan’s mother, the head obstetrician at a Long Island hospital, delivered baby Kerry and knew immediately something was terribly wrong.

“Can you imagine the trauma of it?” he said. “Seeing your new granddaughter come out like that?”

For years, the Ryans were baffled by their daughter’s problems. There had been no history of birth defects on either side of the family. Neither were smokers or drug users. A second child, born a few years later, was relatively healthy. It wasn’t until Maureen Ryan read a magazine article that suggested a link between dioxin and birth defects that it dawned on them that her husband’s tour in Vietnam might be connected to Kerry’s problems.

By that time, there had been reports suggesting that Vietnamese children born in areas heavily contaminated by Agent Orange had high rates of defects, though some U.S. researchers said rigorous scientific studies never established a link.

Mike Ryan also had an ugly rash, called chloracne, that’s considered a signature effect of Agent Orange exposure. He remembered drinking rainwater collected from the tops of tents in Vietnam, not realizing it may have been contaminated with chemicals sprayed from above.

The Ryans went public with their concerns at a press conference in 1978, drawing the nation’s attention to the children of Vietnam veterans.

A year later, the Ryans pushed Kerry into a congressional hearing in a wheelchair to testify about her struggles, prompting then Rep. Al Gore, D-Tennessee, to ask, “I wonder what the reaction of the VA would be if the enemy had used Agent Orange?” In the fall of 1980, President-elect Ronald Reagan arranged a meeting to learn about their struggle and concerns about the herbicide.

But after that, the momentum died.

Instead, in the years that followed, the Reagan administration worked to undermine the Ryans’ cause in court as the couple served as one of the lead plaintiffs in a class-action lawsuit against the chemical companies that made Agent Orange.

When the lawsuit settled in 1984 for $180 million, U.S. District Judge Jack Weinstein ruled that direct payments could only be made to disabled veterans or survivors of those who’d died, cutting off children like Kerry.

Weinstein, who’d expressed doubt that veterans had been harmed, was even more skeptical about their children, writing, “however slight the suggestion of a causal connection between the veterans’ medical problems and Agent Orange exposure, even less evidence supports the existence of an association between birth defects … and exposure of the father to Agent Orange.”

Mike Ryan wasn’t surprised. “I knew we had no shot,” he said.

In 1997, when the VA finally began offering compensation for children with spina bifida, the Ryans didn’t bother applying. Mike Ryan said it was never about the money; it was about recognition of the debt he believes his country owes his daughter. “She has 22 birth defects, and they want to pay only for spina bifida? Come on, give me a break.”

Kerry died in 2006 at the age of 35.

Mike Ryan, now 71, said he hadn’t kept up with scientific advancements that potentially confirm what he’s spent years arguing — that a father’s exposure to toxins can cause health problems in offspring. In the end, it won’t matter what researchers discover, he insisted.

“They will never admit it,” he said, “because if they do, then America is admitting to drafting the unborn.”

The same year Weinstein cited a lack of evidence connecting Agent Orange and birth defects, an Air Force scientist believed he’d found some.

In 1979, a team of researchers had embarked on a $143 million, 20-year study of those Air Force vets who’d had the greatest exposure to Agent Orange: Those who’d sprayed it. The study was extremely detailed, verifying what veterans said with a host of medical exams and biological specimens, including blood, semen and urine samples. Five years in, Dr. Richard Albanese, a lead investigator, and his team made what they considered an intriguing finding — children born to exposed Air Force vets after the war had more defects than children of those who hadn’t handled Agent Orange.

The researchers wrote up the results in a report, but their superiors halted its release, saying more research was needed, including physically examining all the children to verify whether they had birth defects, Albanese recalled in a recent interview. After Albanese spoke up about the delay, he was taken off the project and reassigned.

Finally in 1988, under pressure from members of Congress, the study Albanese had worked on was released, but with only his name on it. His study found “a statistically significant increase in reported birth defects” among veterans who handled Agent Orange. Then, four years later, the Air Force published a follow-up paper that claimed no evidence had been found linking Agent Orange exposure to birth defects in the men’s children.

The 1992 report looked at the data in a different way. If there indeed was an association, the researchers wrote, they would have expected to find that veterans with more dioxin lingering in their blood would have higher rates of birth defects in their children, but that wasn’t the case. They concluded that the few links between dioxin and birth defects “were generally weak, inconsistent or biologically implausible” and the data “provided no support” for such a connection.

To this day, Albanese believes his findings were correct while those of his former colleagues were flawed.

“These people really bent over backwards to try to disprove a connection,” he said. “That’s my feeling.”

Albanese, who now runs a small defense consulting company in San Antonio, said he believes the episode was part of a broader government effort to suppress findings connecting Agent Orange to the health of veterans and their children.

“I’m so sad and so angry that science could be corrupted this way,” said Albanese, who served in the Air Force. “I’m a faithful military man, but this was not honorable behavior.”

Seven years later, some of Albanese’s concerns were investigated by the Government Accountability Office and at a congressional hearing in 2000. The GAO noted the unusual way in which the Air Force report was handled and said one veterans’ organization believed it may have delayed the VA’s decision to provide benefits to children with spina bifida.

Air Force researchers have denied that their findings were manipulated and said they needed the extra time to verify each birth defect against medical records to ensure it was correct.

Meanwhile, thousands of Vietnam vets have added information every year to the VA’s growing body of data, deepening a potentially rich pool for researchers. Yet, for decades, nobody looked.

By 1978, Agent Orange and its potential effects had become a national controversy. In response, the VA began offering veterans free examinations and regular notifications when new information about Agent Orange came to light. As part of the effort, information was gathered about each vet and entered into a newly established Agent Orange Registry.

The questionnaire collected detailed information about veterans’ service, health conditions and possible exposure to herbicides, asking vets whether they handled or sprayed Agent Orange, were directly sprayed with it, were in an area recently sprayed with it, ate or drank food that may have come in contact with it, or were exposed to other herbicides. The VA also collected information about children born before and after the vet’s service with spina bifida or other birth defects.

The questionnaire didn’t define what constitutes a birth defect, leaving it to each vet to do so. In an email last month, the VA said it “would expect” parents to accurately answer questions about whether their children have birth defects, since such defects affect about 3 percent of all births. Yet in its statement on Thursday, the agency said that it anticipated “significant variation in the accuracy” of the self-reported information.

ProPublica looked for differences in birth defect rates among children of veterans who said they were exposed to Agent Orange compared to those who said they weren’t or weren’t sure. The analysis focused on a group of 37,535 veterans who had children born before their service in the war as well as during or after, in part because many of the factors relevant to birth defects wouldn’t change, including the veterans’ genetic makeup.

A veteran was considered exposed if he answered “definitely yes” to the questions about handling or spraying Agent Orange or being directly sprayed with it. Fewer than 10 percent of veterans fit this criteria. If a veteran said he was unsure or definitely was not exposed, he was considered unexposed.

The analysis showed that both groups saw a substantial increase in birth defects among their children born after the war, but the rate was higher for those who were exposed. Slightly more than 13 percent of veterans who sprayed, handled or were sprayed with Agent Orange reported having a child with birth defects born during or after the war, compared to nearly 10 percent of veterans who were not exposed or were unsure. The two groups had similar rates of birth defects among children born before the war, but the odds of having a child born during or after the war with birth defects was 30 percent higher for exposed veterans.

ProPublica ran its methodology by experts in the field, including Michalek, who was involved in the Air Force birth defects study, and Birnbaum, the director of the federal environmental health research agency. The analysis has its limitations, including the self-selected nature of the veterans who took part in the registry and the self-reported information they provided. It also does not prove that Agent Orange caused the increased rate of birth defects, but it does raise important questions for future research, they said.

At one point in the mid-1980s, the VA also saw the research value of its registry, “namely to provide a means of detecting clues or suggestions that specific health problems or unexpected health trends are showing up in this group of veterans,” according to a fact sheet prepared at the time.

Indeed, when a preliminary analysis of the registry in 1983 showed no unusual health problems in Vietnam veterans, Alvin Young, the head of the VA’s Agent Orange Projects Office at the time, announced the results at a news conference, drawing newspaper headlines that suggested Agent Orange hadn’t harmed vets.

Since then, the VA has grown dismissive of the registry’s value. Today the registry is primarily used to keep track of vets’ contact information. In its statement Thursday, the VA said “observation of birth defects was not the primary purpose of the Agent Orange registry.”

“VA has taken a very cautious approach in the use of the registry data, but is currently exploring ways to better utilize this resource for research using administrative records or supporting research recruitment,” the agency said.

Over the past 18 months, more than 6,000 vets and their family members confronting Agent Orange-related issues have shared their stories with ProPublica and The Pilot. Some said it was inexplicable that VA had collected all their information, then simply stashed it away unexamined.

Royal Gee, a Marine Corps veteran from Georgia, completed a registry exam a few years ago. He has rheumatoid arthritis and chronic obstructive pulmonary disease, among other health problems. His daughter born before the war is healthy but the one conceived afterward was born with cysts on her head. She’s had ongoing problems with cysts in her joints and now suffers from an immune system disorder.

“They say it has nothing to do with my service in Vietnam and it stops right there,” he said. “There’s got to be a reason.”

Experts, too, have seen their calls for more research die without explanation.

Federal scientific advisory panels have repeatedly urged the VA to research Agent Orange’s effect on offspring. In 2007, a panel of the prestigious Institute of Medicine said the VA “should review all the possible cognitive and developmental effects in offspring of veterans. Such a review should include the possibility of effects in grandchildren.”

In 2009, 2012 and 2014, other IOM panels reiterated that recommendation and expanded on it.

This year, yet another IOM panel weighed in, reporting no progress on the earlier recommendations and encouraging more research in animals. “To date there has been minimal investigation of whether paternal exposure poses a risk of adverse effects in their offspring,” it said.

Before joining the VA, Linda Schwartz, now the agency’s assistant secretary for policy and planning, looked into birth defects among the children of vets as an associate clinical professor of nursing at Yale University. She and a colleague, George Knafl, reassessed the findings of the Air Force study. They found that, contrary to the main published findings, “there is distinct evidence” that the children of those who handled Agent Orange had more birth defects and developmental disabilities. They presented the work at a 2003 international dioxin meeting, but their manuscript was not accepted for publication in a scientific journal.

Schwartz, in a recent interview, said if the U.S. conceded that Agent Orange caused birth defects, the Vietnamese government might seek compensation for children who’ve been harmed over there. “We ran into a wall,” she said. “People were deathly afraid that the Vietnamese would then lodge a horrendous lawsuit against the United States.”

For now, the VA pays to store the blood, semen and tissue specimens from the former Air Force spray crews in a freezer at a base in Ohio, leaving open the possibility for future studies.

Schwartz’s role at the VA doesn’t put her in charge of such studies. But she said new technology could be used to answer at least some questions. “Maybe it’s not the answer that people want, but at least it would be an answer.”

In the absence of new government research into Agent Orange and birth defects, advocates around the country have pursued their own strategies for drawing attention to the issue.

Heather Bowser was born in 1972, three years after her father, William Morris, returned from Vietnam. His base was less than 10 miles away from Bien Hoa Air Base, which served as the hub for the Air Force crew that sprayed Agent Orange across the country. The airplanes returning from short missions would often dump Agent Orange in the river alongside his base, he told her.

Bowser weighed 3 pounds, 4 ounces at birth. She was born missing her right leg below the knee and several of her fingers. She had no big toe on her left foot, and the remaining toes were webbed. “The doctor said, ‘If they’re that messed up on the outside, they’re usually that messed up on the inside,’” she said. “My parents had no idea. There was no ultrasound and that kind of stuff, so I made quite a shocking entry into the world.”

Five years ago, Bowser co-founded Children of Vietnam Veterans Health Alliance, which has since grown to nearly 4,000 members who swap stories or vent about doctors who dismiss their concerns about Agent Orange. “Our stories are very similar … very similar birth defects, very similar health issues later,” she said. “Neural tube defects, shortened limbs, webbed toes, missing limbs, extra vertebrae, missing vertebrae, autoimmune disorders. The list goes on.”

Bowser, who lives in Canfield, Ohio, said her group has been limited by a lack of funding, but they have reached out to scientists working on the issues in the United States and Vietnam. “I don’t think it’s too late. Quite honestly, it’s not the monetary payoff. It’s the acknowledgement that a parent suffered, we suffered, and something needs to be acknowledged. … This isn’t a figment of your imagination. This isn’t a conspiracy theory. This is something that happened to you and your family.”

Matthew Penner, whose dad is an Army veteran, found Bowser’s group and said reading others’ stories “just blew my mind. That really put it together for me.”

While Bowser has been working to help the children of veterans connect with one another, Mokie Porter has been working to get veterans to share their medical and exposure information with their children in case they don’t live long enough to see a connection made.

Porter is the director of communications for the Vietnam Veterans of America, based in Silver Spring, Maryland. The group has been a forceful advocate for compensating veterans for health problems linked to Agent Orange.

Porter, who has worked there since 1985, said she became particularly interested in vets’ children in 2009 when her own daughter was being treated for cancer at Johns Hopkins Health System. While there, Porter’s daughter befriended the grandson of a Vietnam veteran who also was sick.

After that, she helped launch the VVA project Faces of Agent Orange. They’ve held more than 250 town hall meetings across the U.S., urging veterans to share their families’ stories. At the first one, in Louisville, Kentucky, “the room was filled,” Porter said. “Everybody in the room was surprised that they weren’t alone.”

Porter and her colleagues also encourage the children of veterans to file claims with the VA for benefits related to Agent Orange even though the department currently doesn’t cover most defects. Their hope is that the VA will keep the claims on file, and, should it change its position, pay benefits retroactively.

Since 2001, the VA has received claims for benefits from more than 8,100 people citing spina bifida and other birth defects, an agency spokesman said. Of those, only 1,325 claimants have received benefits.

Porter also serves on the board of Birth Defect Research for Children, which has attempted to gather data on birth defects to be analyzed in a way the VA has not done. It is led by Betty Mekdeci, who first started gathering data on birth defects and environmental exposures in the 1980s after her son was born with health issues, then became fixated on helping the children of Vietnam vets.

She believes her data shows elevated numbers of birth defects — especially those affecting a child’s immune and nervous systems — in offspring of Vietnam veterans, though those findings have not been confirmed in a published study.

“I think if we send young people to war, to defend us, our way of life, whatever, that we have a contract with them,” said Mekdeci, who despite a lack of formal scientific training has presented her findings to Congress and the IOM. “We have a contract to take care of them if they’re injured, and if their children are injured because of their exposures, we have a contract to take care of them, too.”

With the passage of time, hope dims for answers to the questions about Agent Orange and birth defects.

In a report this year, an IOM panel said the military and the VA should set their sights on forward-looking projects, like tracking which chemicals soldiers are exposed to in real time.

“Revisiting what happened 50 years ago, 40 years ago, is essentially impossible,” said Dr. Kenneth Ramos, who chaired that IOM panel, while speaking at a forum this summer in Washington sponsored by ProPublica and The Pilot. “We’re not going to be able to scientifically go back and reconstruct what could have happened 50 years ago.”

In an interview, Michael Skinner, a Washington State University professor of biological sciences and one of the leaders of the study of epigenetics, said he, too, wonders whether it makes sense to delve too deep into the question of Agent Orange and birth defects. He was a co-author on the 2012 paper that found dioxin induces lingering effects in the offspring and future generations of female rats. But he said he hasn’t found additional funds to continue the work in male rats.

Besides, he said, the epidemiology is always going to be complicated. Just because someone’s child or grandchild manifests a health problem linked to dioxin exposure, that doesn’t mean Agent Orange caused it. People could have been exposed to dioxin in a variety of ways because the chemical was prevalent in urban areas in the U.S. until the late 1970s.

“There’s a point at which we have to say, ‘Look, a really bad thing happened, but you have to stop pointing fingers.’”

Such sentiments don’t sit well with veterans or their children. “A lot of people probably don’t think about it because a lot of people don’t want to think about it,” said Ralph Thornburgh, an Army vet whose two daughters born after Vietnam have had health problems, including one with leukemia. “They want to just go about their everyday life.”

The VA is working on a long-awaited study on whether Vietnam veterans, generally, have “different patterns of illness that are unlike their non-Vietnam deployed military counterparts, and members of the U.S. population.” It will also look at the health of their children. It is not specifically looking at effects of Agent Orange, but it has been praised by veterans groups as an important effort.

Schwartz said more needs to be done about Agent Orange and its impact on the children of veterans.

“These individuals deserve an answer,” Schwartz said at the forum hosted by ProPublica and The Pilot. “This is the right thing to do, and although we may not have all of the wonderful information, we have some. Let us at least take a stab at this.”