The prevalence of high-risk human papillomavirus (HR-HPV) has been reported to be three times higher in female sex workers (FSWs) in Callao, Peru than in the general population of women in Peru. Prevalence of HR-HPV among male clients has not yet been reported. A total of 150 men soliciting intercourse in sex work venues submitted questionnaires, samples for sexually transmitted infection (STI) testing, and self-collected penile samples prior to and following intercourse for HPV genotyping. We identified variables associated with pre-coital HR-HPV, and compared HR-HPV detection pre- and post-coitus. Prior to intercourse, HR-HPV prevalence was 41.9%. Married clients were less likely than unmarried clients to have HR-HPV detected (p = 0.03). While post-coital HR-HPV prevalence was higher (47.6%), the difference was not statistically significant. However, there was a significant increase in the mean number of HR-HPV DNA strains detected before (0.75) and after (0.94) intercourse (p = 0.02). No cases of gonorrhoea or syphilis and six (4.1%) cases of chlamydial infection were detected. Despite low prevalence of other STIs, male clients had a high HR-HPV prevalence. The increase in detection of HR-HPV following intercourse demonstrates a potential for transmission of HR-HPV despite high self-reported condom use.