Community-based participatory research (CBPR) has been posited as a promising methodology to address health concerns at the community level, including cancer disparities. However, the major criticism to this approach is the lack of scientific grounded evaluation methods to assess development and implementation of this type of research. This paper describes the process of development and implementation of a participatory evaluation framework within a CBPR program to reduce breast, cervical, and colorectal cancer disparities between African Americans and whites in Alabama and Mississippi as well as lessons learned. The participatory process involved community partners and academicians in a fluid process to identify common ground activities and outcomes. The logic model, a lay friendly approach, was used as the template and clearly outlined the steps to be taken in the evaluation process without sacrificing the rigorousness of the evaluation process. We have learned three major lessons in this process: (1) the importance of constant and open dialogue among partners; (2) flexibility to make changes in the evaluation plan and implementation; and (3) importance of evaluators playing the role of facilitators between the community and academicians. Despite the challenges, we offer a viable approach to evaluation of CBPR programs focusing on cancer disparities