The Pentagon's recent decision to limit anthrax vaccine shots to those at high risk does not address the fundamental objection to the shots, which is the lack of informed consent. The military maintains that it is not required to seek informed consent for the vaccine because it is currently approved by the Food and Drug Administration, and it continues to court-martial personnel who refuse the vaccine. These servicemembers contend that the vaccine is unsafe and that the military is not using it in the prescribed manner.

The Pentagon announced its controversial plan to forcibly inoculate all 2.4 million troops against anthrax in 1997. Almost immediately, military members began to protest, based in part on the revelation that approximately 300,000 servicemembers had been given experimental drugs without their knowledge in the Gulf War. Both during and after the Gulf War, many military personnel experienced systemic medical problems, which are often collectively termed Gulf War Syndrome. Seven years after the Gulf War, the military finally admitted that it had used experimental drugs on its personnel without their consent, and that these drugs could be factors in the medical problems.

The FDA approved the current anthrax vaccine in 1970 primarily for agricultural workers, but not for routine immunization on large populations. Originally approved for a six-shot, eighteen-month protocol, the vaccine is intended to treat cutaneous (through the skin) anthrax, but has never been tested for inhalation anthrax, which is the most deadly form and the most likely to occur in a combat situation. Despite the military's assertions that very few adverse reactions have been reported from the vaccine, the General Accounting Office found that the Pentagon has been negligent in tracking such reactions. In fact, many military personnel have reported adverse reactions. In 2000 the GAO surveyed the National Guard and reserve forces given the vaccine, and 85 percent reported some reactions, with 23.8 percent reported to be systemic. Additionally, the GAO reports that the long-term effects of the anthrax vaccine have never been studied. In 1994 one of the Army's top biological researchers wrote that "the current vaccine against anthrax is unsatisfactory."

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