BACKGROUND: There have been several barriers in effectively engaging men who have sex with men for STI/HIV prevention and treatment programming in Nigeria including social stigma, policies, and laws criminalizing same-sex practices. The objective of this study was to describe the human rights context for MSM in Abuja and characterize factors associated with having had a genital ulcer disease in the previous 12 months, a health outcome associated with increased risk of HIV acquisition and transmission. METHODS: A convenience sample of 297 men reporting ever having had anal intercourse with another man participated in the study in 2008. A structured survey instrument including sexual risk behaviour for STI/HIV, disclosure of sexual orientation, perceived and enacted human rights violations were performed. Descriptive and inferential data analyses were conducted using Stata11 software. RESULTS: 36% reported having been discriminated due to sexual orientation and 17% reported being afraid to walk the streets of their community. Enacted rights violations included 41% having been blackmailed, 36% been beaten, 13% been denied housing, and 11% been jailed due to sexual orientation. Having been blackmailed due to sexual orientation (aOR 3.40, 95%CI: 1.35-8.56) was significantly associated with reporting having had a genital ulcer in the last 12 months. Having been beaten due to sexual orientation (aOR 2.36, 95%CI:0.96-5.82) was moderately significantly associated with reporting having had a genital ulcer in the last 12 months. CONCLUSIONS: High levels of experienced stigma, discrimination and human rights violations among MSM in Abuja was reported, constituting structural risks that are linked to sexual risk behaviour for STI/HIV. Given data on the high prevalence and incidence of HIV among MSM in Abuja, these findings reinforce the need for structural interventions to mediate access to STI/HIV prevention and treatment services.