Limited data exist on the effect of clinical trial participation on sexual behavioural change. Two hundred female sex workers working in Lima, Peru received human papillomavirus (HPV) vaccine in either the standard (0, 2, 6 months) or modified (0, 3, 6 months) schedule. Participants received comprehensive screening and treatment for sexually transmitted infections (STIs), counselling on safe sex practices, education about HPV and the HPV vaccine, contraceptives (oral and condoms) and family planning at each visit. We assessed vaccine completion rates, change in sexual practices, and changes in HPV knowledge before and after participation in the vaccine trial. There were high rates of vaccine completion, 91% overall. The estimated number of reported new and total clients over a 30-day period decreased significantly (P < 0.001). Knowledge about HPV and HPV-related disease increased among all participants. In addition, all participants listed at least one preventive strategy during the month 7 follow-up survey.