Anal human papillomavirus (HPV) is prevalent among men who have sex with men (MSM), but has not been studied in the Russian Federation. A cross-sectional survey and HPV genotyping were conducted among HIV seropositive (n=58) and seronegative MSM (n=65)in Moscow. Multivariable logistic regression was performed to identify correlates of infection with oncogenic HPV genotypes 16 and/or 18 (HPV 16/18). Forty per cent (49/124) of all MSM were infected with at least one anal HPV genotype, 31.5% (39/124) had HPV16/18,and 11.5% (14/121) had high-grade squamous intraepithelial lesions (HSIL). HPV 16/18 was more prevalent in HIV seropositive than seronegative men (24/58,41.4% vs 15/65, 23.1%; p=0.03). HIV infection was independently associated with HPV 16/18 (adjusted odds ratio (AOR): 5.08; 95% confidence intervals (CI):1.49-17.34, p=0.01), as was having 2-4 steady male sex partners in the last year (vs ≤ 1 partner; AOR: 6.99;95%CI: 1.94–25.24, p<0.01). History of prison/detention,migration to/within Russia and use of incompatible lubricants were marginally associated with HPV16/18 (p<0.10). Comprehensive prevention options are needed to address HIV and HPV infection among MSM in Russia and may benefit from inclusion of young men in piloted HPV vaccination programmes.