This analysis describes the nature of community participation in National Institutes of Health and Centers for Disease Control and Prevention funded community-based participatory research (CBPR) projects, and explores the scientific and social implications of variation in community participation. We conducted in-depth interviews in 2012 with professional and community researchers from 25 CBPR projects in the Southeast US. Interview topics focused on participants' experiences with the nature and conduct of their CBPR project. Projects were rated on community participation in 13 components of research. Projects varied substantially in community participation. Some projects had community participation in only two to three components; others had participation in every component. Some professional researchers were deliberate in their inclusion of community participation in all aspects of research, others had community participation in some aspects, and others were mainly concerned that community members had the opportunity to participate in the study. Findings suggest a need for a standardized rubric for community-based research that facilitates delineation of approaches and procedures that are effective and efficient. Little actual community participation may also result in negative social impacts for communities.