Background: High-risk human papillomavirus (hrHPV) is a leading cause of anogenital cancers and disproportionately affects men who have sex with men (MSM), particularly in low-and middle-income countries. Few studies in sub-Saharan Africa have concurrently examined penile and rectal hrHPV infection and their site-specific behavioral and biological correlates. We assessed the prevalence, genotype distribution, and factors associated with penile and rectal hrHPV among MSM in Kisumu, Kenya.  Methods: We conducted a cross-sectional analysis of baseline data from MSM aged 18–35 years. Clinician-collected penile and rectal swabs were tested for hrHPV using the ScreenFire HPV assay. Urine and rectal specimens were tested for Chlamydia trachomatis and Neisseria gonorrhoeae using GeneXpert, and HIV status was confirmed as per Kenyan national guidelines. hrHPV was analyzed separately by anatomical site. Log-binomial regression was used to estimate adjusted prevalence ratios (aPR) for associations with sociodemographic, behavioral, and biological factors.  Results: Penile hrHPV prevalence was 24.7% (39/158) and rectal hrHPV prevalence was 12.5% (22/176); 6.7% of participants tested at both sites had dual-site infection. Most infections at both sites involved a single genotype group. HPV-18/45 was the most common genotype group at both sites. Penile hrHPV was more likely among participants with HIV (aPR=2.27, p=0.050) and those reporting insertive anal sex (aPR=5.26, p=0.062), and was less common among employed participants (aPR=0.25, p=0.048). Circumcision showed a protective trend (aPR=0.52, p=0.090). Rectal hrHPV was more common among participants with rectal chlamydia and/or gonorrhea infection (aPR=3.34, p=0.001), transgender or non-binary identity (aPR=2.28, p=0.036), and receptive anal intercourse (aPR=3.97, p=0.062). Although HIV was associated with rectal hrHPV in unadjusted analyses, this relationship was attenuated after accounting for rectal bacterial STI infection.  Conclusions: hrHPV infection was common among MSM in Kisumu, Kenya, with distinct site-specific correlates. The strong association between rectal bacterial STIs and rectal hrHPV highlights the need for integrated HPV and STI screening. These findings support expansion of gender-neutral HPV vaccination and etiologic STI screening to reduce HPV-associated cancer risk among MSM in sub-Saharan Africa.