Her thesis alleges a connection between vaccinations and autism, a claim that was already convincingly refuted, and false claims that vaccines do not control whooping cough. By 2009, Wilyman was a member of the Australian Vaccination-risks Network (AVN), an anti-vaccination group, and coordinates two anti-vaccination groups; Vaccination Decisions and Vaccination Choice. In 2011 Wilyman opposed the cancer-preventing HPV vaccination saying evidence about the vaccine's benefits were not clear, and it was reported that she claimed that vaccinations are linked to autism. HPV vaccination has significantly reduced rates of cervical cancer, and is thought to have the potential to eliminate it altogether. In 2012 she caused controversy after the death of a child from whooping cough, questioning "whether the family had been paid to use their daughter's death to promote vaccine", causing the family of the deceased to request that Wilyman not use their daughter's death in furthering her agenda. In 2013, the Australian Medical Association (AMA) criticised the university's decision to fund Wilyman to attend a conference in the US. Wilyman was provided with $3,000 by the university to present a paper opposing human papillomavirus (HPV) vaccinations. The conference was organised by predatory open access publishing company OMICS Publishing Group, which has also been criticised for running predatory meetings with no effective standards for speaker selection. In response to the criticism of Wilyman's trip, the university's Dean of Research, Tim Marchant, stated that the university upheld the principles of academic freedom and, accordingly, it was important to support Wilyman and the presentation of differing viewpoints, even when they were controversial. Brian Martin, who was supervising Wilyman's research, also supported the decision, arguing that attending the conference was a valuable experience for Wilyman. Questions of misconduct concerning Wilyman's Masters thesis were raised in 2014, and were investigated and cleared in 2015. "The Australian" reported that "Wilyman [was] shielded from critics" by the university in 2014 when their media office refused a request to promote the 44th Annual Scientific Meeting of the Australasian Society for Immunology, to be held at a Novotel Hotel in Wollongong. The reason given was that, if the conference "will be discussing vaccinations, we should steer well clear of doing any publicity. We don't want to inflame any opponents of ... Judy Wilyman." According to the university, they were attempting to limit "the vicious and repeated attacks being directed ... towards a then student"  Wilyman entered a PhD a program in 2007 in the same UOW Faculty as awarded her Masters, but with her research focus expanded to cover Australian vaccination policy more generally.