Guatemalan gay and bisexual men, men who have sex with men (MSM), and transgender persons carry disproportionate burden of HIV and other sexually transmitted infections compared with other Guatemalan subgroups. However, little is known about the determinants of sexual health to inform health promotion and disease prevention interventions among these sexual minorities. We sought to explore sexual health and HIV risk among Guatemalan sexual minorities, using a community-based participatory research approach. We conducted 8 focus groups (n = 87 participants total) and 10 individual in-depth interviews with gay and bisexual men, MSM, and transgender persons. Using constant comparison, an approach to grounded theory, we analyzed verbatim transcripts and identified 24 themes that we organized into five ecological factors influencing sexual health: intrapersonal (e.g. misconceptions about HIV transmission, low perceived susceptibility and lack of condoms use skills); interpersonal (e.g. family rejection and condom use as a barrier to intimacy); community (e.g. discrimination and stigma); institutional (e.g. limited access to health promotion resources); and public policy (e.g. perceived lack of provider confidentiality and anti-gay rhetoric). There is profound need for multiple-level interventions to ensure that Guatemalan sexual minorities have the knowledge and skills needed to reduce sexual risk. Interventions are warranted to increase social support among sexual minorities, reduce negative perspectives about sexual minorities, develop institutional resources to meet the needs of sexual minorities and reduce harmful anti-gay rhetoric. Understanding and intervening on the identified factors is especially important given that the health of Guatemalan sexual minorities has been to-date neglected.