Congregation-based health program evaluations often rely on surveys, but little documentation is available regarding specific methods and challenges. Here we describe methods used to achieve acceptable response rates (73-79%) in a survey of HIV-related attitudes and behaviors in two African American and three Latino churches in high HIV-prevalence communities in Los Angeles County. Survey participation was enhanced by conducting survey sessions at church-based meetings (e.g., women's Bible study) and after worship services; employing diverse survey staff; providing participation incentives for pastors, church coordinators, and survey participants; and working collaboratively and respectfully with congregational leaders. Achieving broad participation in church-based surveys on sensitive health topics is feasible when done collaboratively with congregational leaders and with a flexible protocol, which permits tailoring survey approaches to cultural and organizational contexts and leverages available resources appropriately.