Anogenital warts caused by human papillomavirus are common in sexual and gender minorities (SGM). The prevalence of, and factors associated with warts were described for SGM with a high burden of HIV in Nigeria. Individuals who reported anal sex with men were enrolled in the TRUST/RV368 cohort. Participants completed an interviewer-led survey, provided biological samples, and had a physical examination. Specific to the Lagos site, clinic staff offered standardized warts treatment services. RDS-weighted multivariable logistic regression was used to estimate the adjusted odds ratios (AORs) and 95% confidence intervals (CIs) for factors potentially associated with anogenital warts. Of 672 enrolled SGM, 478 (71%) engaged in warts services and had complete data. The median age (interquartile range) was 22 (20–26) years, 272 (52%) initiated sex before age 18, and 347 (79%) were cisgender men. Multiple male sexual partners in the previous year were reported by 448 (90%) of the participants, and 342 (66%) were living with HIV. Warts were diagnosed in 252 (54%), including anal warts in 234 (43%) and penile warts in 44 (8%); 26 (5%) had both anal and penile warts. Factors independently associated with warts included HIV (AOR:2.97; CI:1.44–6.14), engaging in receptive anal sex (AOR:3.49; CI:1.25–9.75), having multiple male sexual partners (AOR:7.26; CI:2.11–24.87), age at sexual debut (AOR:0.53; CI:0.28–0.98), and non-binary gender identity (AOR:0.20; CI:0.05–0.71). Warts were common among SGM in Nigeria, particularly those living with HIV. Administration of HPV vaccination before sexual debut or as a catch-up vaccination may prevent HPV-associated complications.