Men who have sex with men (MSM) are a crucial and marginalized at risk population for HIV in Africa but are poorly studied. Like other areas of Africa, homosexuality is illegal in Kenya. We assessed MSM comfort in accessing health services and willingness to participate in HIV prevention research in Kisumu, Kenya—an area of high HIV prevalence. We conducted a two-phase formative study with individual interviews (n = 15) and a structured survey (n = 51). Peer contact or snowball method (n = 43, 84.3%) was the primary recruitment strategy used to locate MSM. Exact logistic regression models were used for survey data analysis. Over 60% (32/51) of survey participants were not very comfortable seeking health services from a public hospital. Almost all MSM (49/51; 96.1%) reported willingness to be contacted to participate in future HIV research studies. Efforts to provide facilities that offer safe and confidential health services and health education for MSM is required. Continued community engagement with the MSM population in Kenya is needed to guide best practices for involving them in HIV prevention research.