"While the policy of submitting comments on an agency's proposed order may be unusual, it is the course the agency chose to take and this Court shall ensure that the agency follows through its commitment to the public," Sullivan wrote. "By refusing to give the American public an opportunity to submit meaningful comments on the anthrax vaccine's classification, the agency violated the Administrative Procedure Act."

That's the administrative argument. But lurking beneath the surface of the case is the larger suspicion by critics that the vaccine is simply unsafe and is causing members of the military to become seriously ill -- that instead of boosting the immune system, the vaccine in some cases is triggering a violent and sometimes deadly physical reaction.

The anthrax program has been marked by controversy since its inception in 1998, when the Pentagon during the Clinton administration announced it would inoculate its 2.4 million service members, both active and reserve, as part of a multibillion-dollar biowarfare defense program. Citing health concerns, some members of the military objected. To date, approximately 1.2 million members of the military have been given the anthrax vaccine.

In 1999, when Air Force Reserve pilots were required to take the vaccine at Dover Air Force Base in Delaware, 55 pilots out of 120 in the Reserve wing stationed there refused and then resigned. Many were full-time commercial pilots who feared that the vaccine's side effects would end their aviating careers.

In the fall of 2000, then candidate George W. Bush announced, "I don't feel the current administration's anthrax immunization program has taken into account the effect of this program on the soldiers in our military and their families. Under my administration, soldiers and their families will be taken into consideration." There are indications that, urged by strategist Karl Rove, who was concerned about the political ramifications, the Bush administration early on tried to address the problems surrounding the vaccinations and do away with the mandatory program. But then came the terrorist attacks of Sept. 11 and the subsequent anthrax deaths, followed by the run-up to war with Iraq, which was framed as a battle over WMD. Suddenly, instead of trying to eliminate the vaccination program, the Bush administration accelerated its implementation.

But the controversy has continued to grow. In 2001, Connecticut's attorney general, concerned the state might bear responsibility if its National Guardsmen got sick from the vaccine, wrote the Department of Defense and the FDA urging them to abandon the program. That same year, John Buck, an Air Force captain, became the first military physician court-martialed for refusing to take the anthrax shot. Soon after he refused, he met with an Air Force superior and talked about how he couldn't, in good conscience, take the vaccine if he didn't believe in the quality of the science behind it. "At one point the commander said, 'Son, sometimes you have to check your integrity at the front door.' I about fell out of my chair," Buck told Salon last year.

Also in 2001, during the anthrax scare on Capitol Hill, Senate Majority Leader Bill Frist, R-Tenn., a physician, urged Senate staffers not to take the vaccine because "there are too many side effects." (Some doctors think it's safer to take antibiotics after being exposed to anthrax than to be vaccinated in advance.)

This month, the Delaware News Journal has published an exhaustive investigation into the anthrax vaccine controversy, centering its attention on Dover, Del. The paper reported that "troops received anthrax vaccine starting in 1999 that may have contained squalene, a substance that can be used to increase the potency of vaccine. Some researchers believe that even trace amounts of squalene can suppress the immune system, causing arthritis, neurological problems, memory loss and incapacitating migraine headaches."

Squalene is a fatlike substance that occurs naturally in the body, but some scientists argue that injecting even trace amounts can cause serious illness. According to the News Journal, testing by the FDA in 2000 detected squalene in varying amounts in the vaccine used at Dover. The paper reported, "The military has secretly experimented with squalene to test its ability to boost the effectiveness of some vaccines. The Department of Defense has admitted conducting tests on humans using squalene in vaccines in Thailand. But the military said any contamination in the vaccine in Dover must have occurred accidentally."

On Oct. 10, the paper quoted a former Dover commander who halted the vaccine program after the rash of baffling illnesses as saying, "In my opinion, there was illegal medical experimentation going on."

The anthrax vaccine controversy has not been confined to the United States. In Britain, where the shot is voluntary for troops, roughly half of those deployed in Iraq have refused the vaccine. On the eve of the war with Iraq, the president of the Australian Medical Association announced that in her opinion no definitive scientific evidence showed that the anthrax vaccine was safe. And in a 2000 court-martial case, Canada's top military judge ruled a soldier could refuse the vaccination on the grounds that it amounted to unsafe medical treatment.

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