This case study is based on our work with community-based participatory research with lesbian, gay, bisexual, transgender, and queer communities in Alabama and Mississippi. We describe the process of conducting community-based participatory research in this population, with particular focus on some of the obstacles to success, and some of the strategies that were useful for our work. We discuss the institutional review board process for this study, the process of identifying and recruiting community researchers, our process of providing research training, and the analytic process for this work. In particular, we describe the steps we took to present our study to the institutional review board to ensure clarity and ethical compliance. We articulate our recruitment strategies, including coordination with community organizations, and the use of social media for recruiting. We describe the process we undertook to train community members in research ethics and interviewing skills. Finally, we describe the process we are involved in for data analysis that includes community collaboration. Our goal is to provide a case study which can be useful for those considering a community-involved approach to understanding marginalized populations.