BACKGROUND: In the context of a generalized epidemic and criminalization of homosexuality, men who have sex with men (MSM) in Malawi have a disproportionate burden of HIV compared to other adults. Past research has documented low uptake of HIV prevention and health services among MSM, self-reported fear of seeking health services, and concerns of disclosure of sexual orientation and discrimination in health settings. Qualitative research was conducted among MSM and health service providers in Blantyre, Malawi to understand underlying factors related to disclosure and health seeking behaviors and inform the development of a community-based comprehensive HIV prevention intervention. METHODS: Using peer recruitment, eight MSM participants representing a range of ages, orientations, and social and behavioral characteristics were enrolled for in-depth interviews. Five service providers were recruited from the district hospital, local health and STI clinics, and a HIV prevention service organization. We use the Health Belief Model as a framework to interpret the influential factors on 1) health seeking and uptake among MSM, and 2) influences on provision of services by healthcare providers for MSM. RESULTS: Results highlight disclosure fears among MSM and, among providers, a lack of awareness and self-efficacy to provide care in the face of limited information and political support. Service providers reported concerns of adverse repercussions related to the provision of services to men in same sex sexual relationships. Some MSM demonstrated awareness of HIV risk but believed that within the wider MSM community, there was a general lack of HIV information for MSM, low awareness of appropriate prevention, and low perception of risks related to HIV infection. CONCLUSIONS: Qualitative research highlights the need for appropriate information on both HIV risks and acceptable, effective HIV prevention options for MSM. Information and educational opportunities should be available to the wider MSM community and the health sector. Health sector interventions may serve to increase cultural and clinical competency to address health problems experienced by MSM. To ensure availability and use of services in light of the criminalization and stigmatization of same sex practices, there is need to increase the safety of uptake and provision of these services for MSM.