[2] In 1974, Stewart was part of a government-appointed team tasked with investigating experimental, now-banned whooping cough vaccines given by the British government to orphans and mentally handicapped children.
[9][10] In 1977, he published a paper citing the cases of many of these children as proof that the DPT vaccine caused brain damage.
[12] In the mid-1980s, Stewart served as the lead witness for the prosecution in the case of Johnnie Kinnear, whose mental development was allegedly stunted due to his receipt of the pertussis vaccine.
The case unraveled after contradictions were revealed between Kinnear's parents' testimony and hospital records, and Stewart's role in the pertussis vaccine controversy came to an end as a result.
[8] A former World Health Organization advisor on AIDS, Stewart was described as one of two HIV/AIDS "dissidents to a degree" by the Guardian in 2000 (the other being Andrew Herxheimer).
Epidemiologist Roy M. Anderson dismissed this claim, arguing that Stewart "would benefit from becoming aware of the scientific literature".
[6] In 1995, he argued against giving azidothymidine to pregnant women who had AIDS, even though it had already been shown to be effective at preventing mother-to-child transmission of HIV.
[12] In 1997, he co-authored an article in Current Medical Research and Opinion along with several HIV/AIDS denialists, including Eleni Papadopulos-Eleopulos of the Perth Group.