This paper addresses the issue of whether men who have sex with men (MSM) will share the spectacular reductions in human papillomavirus (HPV) infection and its associated neoplasia that we are currently witnessing in heterosexuals. The reproductive rate for HPV infection in heterosexuals is not well established, but 70% vaccination coverage in women has resulted in a fall of more than 90% in genital warts and HPV types 16/18 in young women and 80% fall in young men indicating that the critical vaccination threshold has been exceeded for this group. Published data on the three elements of the reproductive rate for HPV infection (i.e. transmission probability per sexual partnership, rate of partner change and duration of infectiousness) suggest they are higher in MSM than heterosexuals. This indicates that the reproductive rate for HPV will be higher in MSM and hence the critical vaccination threshold will also be higher. But while vaccinating 70% of girls protect 70% of sexual partnerships in heterosexuals, vaccinating 70% of boys protect more than 70% of partnerships in MSM. Only 9% (30% by 30%) of sexual partnerships in MSM are not protected with 70% coverage. Therefore vaccinating 70% of boys will protect 91% of sexual partnerships in MSM. However the efficacy of the HPV vaccine is much lower when sexually active MSM are vaccinated rather than boys. We argue that if MSM are to have the same benefit from the HPV vaccine that heterosexuals had, boys and not adult MSM will need to be vaccinated.