Objective We describe the formulation and implementation of a participatory evaluation plan for three Transdisciplinary Collaborative Centers for Health Disparities Research funded by the National Institute of Minority Health and Health Disparities. Methods Although different in scope of work, all three centers share a common goal of establishing sustainable centers in health disparities science in three priority areas – social determinants of health, men's health research, and health policy research. Results The logic model guides the process, impact, and outcome evaluation. Emphasis is placed on process evaluation in order to establish a “blue print” that can guide other efforts as well as assure that activities are being implemented as planned. Conclusion We have learned three major lessons in this process: (1) Significant engagement, participation, and commitment of all involved is critical for the evaluation process; (2) Having a “roadmap” (logic model) and “directions” (evaluation worksheets) are instrumental in getting members from different backgrounds to follow the same path; and (3) Participation of the evaluator in the leadership and core meetings facilitates continuous feedback.