Community-based participatory research; community health research; health disparities; process issues Background: Since 2007, the National Congress of American Indians (NCAI) Policy Research Center (PRC) has partnered with the Universities of New Mexico and Washington to study the science of community-based participatory research (CBPR). Our goal is to identify facilitators and barriers to effective community academic partnerships in American Indian and other communities, which face health disparities. Objectives: We have described herein the scientific design of our National Institutes of Health (NIH)-funded study (2009-2013) and lessons learned by having a strong community partner leading the research efforts. Methods: The research team is implementing a mixed-methods study involving a survey of principal investigators (PIs) and partners across the nation and in-depth case studies of CBPR projects. Results: We present preliminary findings on methods and measures for community-engaged research and eight lessons learned thus far regarding partnership evaluation, advisory councils, historical trust, research capacity development of community partner, advocacy, honoring each other, messaging, and finding. Conclusions: Study methodologies and lessons learned can help community academic research partnerships translate research in communities.