Background. We aimed to assess whether sexual exposure may explain all incident anal human papillomavirus (HPV) detections among men who have sex with men (MSM). Methods. A longitudinal study among MSM was conducted between 2010 and 2013 with visits every 6 months and up to 24 months of follow-up. Risk-factor questionnaires, blood samples, and anal and penile self-swabs were collected at each visit. Self-swabs were used for detection and genotyping of HPV by the broad spectrum L1 based SPF10 PCR DNA/enzyme immunoassay LiPA25 system. Serum samples were tested for high-risk HPV (hrHPV) antibodies. Incident anal HPV detection rates among sexually non-, low, and highly exposed MSM were compared. Factors associated with incident anal hrHPV detection were assessed using multivariable Cox regression. Results. Seven hundred fourteen men (median age, 40 years; 39% human immunodeficiency virus [HIV] infected) were included in the analysis. Incident anal detections of all hrHPV types were observed among both sexually nonexposed and exposed MSM. In multivariable analyses, being highly sexually exposed, being HIV infected, and having a penile HPV infection were positively associated with incident anal HPV detection; those reporting more sex partners had a nonsignificantly increased risk of HPV detection. Conclusions. Incident anal hrHPV detection is common among recently nonexposed MSM, suggesting that a reactivated latent HPV infection instead of an incident infection may underlie incident HPV detection.