The human papillomavirus (HPV) vaccine has been linked to a number of serious adverse reactions. The range of symptoms is diverse and they develop in a multi-layered manner over an extended period of time. The argument for the safety and effectiveness of the HPV vaccine overlooks the following flaws: (i) no consideration is given to the genetic basis of autoimmune diseases, and arguments that do not take this into account cannot assure the safety of the vaccine; (ii) the immune evasion mechanisms of HPV, which require the HPV vaccine to maintain an extraordinarily high antibody level for a long period of time for it to be effective, are disregarded; and (iii) the limitations of effectiveness of the vaccine. We also discuss various issues that came up in the course of developing, promoting and distributing the vaccine, as well as the pitfalls encountered in monitoring adverse events and epidemiological verification.