Faith and public health partnerships offer promise to addressing health disparities, but examples that incorporate African-Americans and Latino congregations are lacking. Here we present results from developing a multi-ethnic, multi-denominational faith and public health partnership to address health disparities through community-based participatory research (CBPR), focusing on several key issues: (1) the multi-layered governance structure and activities to establish the partnership and identify initial health priority (obesity), (2) characteristics of the congregations recruited to partnership (n = 66), and (3) the lessons learned from participating congregations' past work on obesity that informed the development of a multi-level, multi-component, church-based intervention. Having diverse staff with deep ties in the faith community, both among researchers and the primary community partner agency, was key to recruiting African-American and Latino churches. Involvement by local health department and community health clinic personnel provided technical expertise and support regarding health data and clinical resources. Selecting a health issue-obesity-that affected all subgroups (e.g., African-Americans and Latinos, women and men, children and adults) garnered high enthusiasm among partners, as did including some innovative aspects such as a text/e-mail messaging component and a community mapping exercise to identify issues for advocacy. Funding that allowed for an extensive community engagement and planning process was key to successfully implementing a CBPR approach. Building partnerships through which multiple CBPR initiatives can be done offers efficiencies and sustainability in terms of programmatic activities, though long-term infrastructure grants, institutional support, and non-research funding from local foundations and health systems are likely needed.