Human papillomavirus (HPV) prevalence was estimated from 2,705 sexually active, uncircumcised, human immunodeficiency virus seronegative men aged 17-28 years in Kisumu, Kenya. HPV prevalence was 51.1% (95% confidence interval: 49.2-53.0%) in penile cells from the glans/coronal sulcus and/or shaft. HPV prevalence varied by anatomical site, with 46.5% positivity in the glans/coronal sulcus compared with 19.1% in the shaft (p < 0.0001). High-risk HPV was detected in 31.2% of glans and 12.3% of shaft samples (p < 0.0001). HPV16 was the most common type and 29.2% of men were infected with more than one HPV type. Risk factors for HPV infection included presence of C. trachomatis, N. gonorrhea, self-reported sexually transmitted infections, and less frequent bathing. Lifetime number of sexual partners and herpes simplex virus type-2 seropositivity were also marginally associated with HPV infection.