Since Persian Gulf War II began about 6,000 soldiers have been shipped home for recovery. Of these, 1,200 were wounded in combat.

Many of the others consider themselves part of an army of "walking dead" – troops who appear to be so physically and mentally exhausted that the military has no recourse but to discharge them.

Why they are ill has become a matter of intense debate inside the Pentagon. Some claim a series of anthrax and smallpox vaccinations made them so gravely ill that they have trouble breathing or sleeping and have experienced a loss of memory. Others have been diagnosed with lupus and heart problems.

At least six died shortly after rolling up their sleeves to receive the anthrax and smallpox shots. But the Pentagon dismissed related claims with such regularity and intimidation that many GIs tell Insight they no longer report the illness. They are told to "suck it up" and move on.

"Don't blame the vaccinations" has been a Pentagon mantra since it began inoculating nearly half a million troops almost two years ago and pumping millions of dollars into BioPort Corp., the Lansing, Mich.-based sole supplier of the anthrax vaccine.

But an alarming outbreak of more than 100 suspected pneumonia cases among Gulf War II veterans serving in Iraq and southwestern Asia has drawn the ire of Congress.

Rep. Chris Shays, R-Conn., held eight congressional hearings on the safety of the vaccination while chairman of the House Government Reform subcommittee on National Security, Emerging Threats and International Relations, and issued a seething report that found serious safety and regulatory problems with the vaccine. Now Shays is asking again, "Could these vaccinations be hurting our troops?"

The Pentagon reluctantly admitted that two Army soldiers – Spc. Joshua M. Neusche, 20, of Montreal, Mo., and Sgt. Michael L. Tosto, 24, of Apex, N.C. - died from complications arising from pneumonia on July 12 and June 17, respectively. The Army is investigating their deaths. Between 1998 and 2001, the U.S. Army Center for Health Promotion and Preventive Medicine reported 17 soldiers died from complications of pneumonia. The Pentagon has confirmed that this year at least 17 others have been placed on respirators but insists the vaccinations have nothing to do with the deaths or illness.

The two pneumonia-related deaths reported recently apparently are an understatement. Family members of Army Spc. Zeferino E. Culunga, 20, of Bellville, Texas, and Staff Sgt. Richard S. Eaton, 37, of Guilford, Conn., claim their sons died in August after being diagnosed with pneumonia. A third death involved Spc. Rachael Lacy of Lynwood, Ill. According to her autopsy, "smallpox and anthrax vaccinations" contributed to her death on April 4 after she first had been diagnosed with pneumonia.

When the victims' families reached out to Defense Secretary Donald Rumsfeld, he ordered a team of military investigators to Germany and Iraq to review the recent pneumonia cases.

"We as a family are concerned that we are not being told the truth," wrote the family of Spc. Neusche in an Aug. 12 letter to Rumsfeld. Like the other families, they asked to see medical records in an effort to get a second opinion on the cause of death. Culunga died of acute leukemia. Lacy was never deployed, so she is not considered part of the cluster of pneumonia cases.

"It is our right to receive truthful, honest and unfiltered answers just as the military required truth, honesty and commitment from our son," says the Neusche-family letter to Rumsfeld.

But the Army is not investigating the deaths of Culunga or Lacy, and is awaiting autopsy results for Eaton.

Besides those who died from pneumonia-like complications, families of six others claim the vaccinations contributed to their sons' deaths – including two who committed suicide because, say the complaints, the vaccinations made them so seriously ill that it destroyed their will to live.

While the U.S. Food and Drug Administration has acknowledged the nature of these deaths, the Pentagon has not because military doctors have refused to confirm that the vaccines contributed to the deaths of any of these victims.

Despite mounting criticism, the Pentagon repeatedly claimed the pneumonia cases had nothing to do with the anthrax or smallpox vaccinations.

"In 200 years of vaccination, no vaccine has ever been shown to cause pneumonia, and there are multiple reasons to believe that the vaccines have no role," Col. John D. Grabenstein, deputy director for clinical operations at the Military Vaccine Agency, told United Press International.

Could Grabenstein be wrong? During congressional hearings on the vaccination program in 1999, Pentagon officials acknowledged there had been three reports of serious illness coincidentally associated with the vaccination involving hypersensitivity pneumonia. A study last year in Pharmacoepidemiolgy and Drug Safety said the vaccine was the cause of pneumonia in two soldiers.

But Grabenstein dismisses such evidence. In fact, in his recent study of vaccination patients published in the Journal of the American Medical Association, or JAMA, he insists there have been no deaths related to the smallpox shot. He ignores the Lacy case because she was never deployed overseas.

"Totally bogus," says Meryl Nass, a civilian doctor who has treated soldiers who became ill after receiving the vaccinations. "I e-mailed JAMA a copy of the death certificate for Lacy. I asked him why he didn't report it. He said, 'We don't accept diagnoses from outside the military.' The Mayo Clinic [in Rochester, Minn.] did the autopsy. They don't believe the Mayo Clinic!"

In fact, Lacy's death is not even listed in the military's Noteworthy Adverse Events report – an omission that critics suggest smells of cover-up.

"My concern regarding the Lacy case is that it was parsed to death in an effort to keep it out of the official reports," says Jeffrey Sartin, a former U.S. Air Force doctor who now works in the Infectious Disease Department at the Gunderson Clinic in La Crosse, Wis. "If it could not be proven with 100 percent certainty that vaccines caused her illness, it was not going to be reported as such."

While Sartin says it should have been reported, Nass wonders if Grabenstein may have a serious conflict of interest that has prevented him from reporting such incidents. She notes Grabenstein sits on a number of pharmaceutical boards and is well known for advocating legislation that would allow pharmacists to administer vaccinations.

Some civilian doctors charge that the Pentagon mislabeled these cases in an effort to avoid making adverse-reaction reports that the military keeps to monitor vaccination programs.

Indeed, Lacy may not be the only death overlooked. The death of NBC correspondent David Bloom, who died of a blood clot after receiving vaccination shots, as well as the death of a 55-year-old Missouri National Guardsman who had a heart attack under similar circumstances, also were disregarded.

"I am not sure they had pneumonia," Nass says. "They are trying to obscure it. They have something else in the lungs and they're not telling us what it is. The Pentagon knows something, but they are not sharing it. And if it isn't pneumonia, what is it?"

What is known is that about one-half of these military patients with pneumonia also had elevated eosinophils in their blood. Eosinophils are responsible for allergic reactions and also help defend against parasites, says Sartin, who worked with a team of doctors that treated Lacy.

"Elevated eosinophils were seen in the blood count of Rachael Lacy before she died, and both her autopsy and the heart biopsy of a servicemember who had myopericarditis showed eosinophilic infiltration of heart tissue," reports Sartin. "This suggests to me the possibility of an immune-mediated reaction to something such as a vaccine."

Another possibility, he says, could be Churg-Strauss syndrome, an autoimmune disease in which "you get asthma, pulmonary infiltrates [in other words, the chest X-ray can look like pneumonia] and eosinophilia." Sartin reports this can lead to vasculitis, which is what killed Bioport employee Richard Dunn. A coroner claimed the anthrax vaccine contributed to Dunn's death.

"If we could get the test results on these patients, and in particular the autopsy results on Neusche and Tosto, we might be able to draw some conclusions about what caused their illnesses and whether it was vaccine-related," he believes.

Pointing to the sharing of information on the SARS outbreak and how that helped civilian doctors diagnose and treat the disease, Sartin argues that the same could be done with data about the sick soldiers. However, for now, the military would rather keep those records under wraps, which puzzles Sartin.

"All of us close to the [Lacy] case, including her family members, wonder why a perfectly healthy young woman, in the top 10 percent of her PT [physical-training] testing, would get sick right after her vaccinations without any other explanation and the authorities would not consider that the vaccine probably, or at least possibly, caused her illness and death."