The Center for Alaska Native Health Research (CANHR) is a community-based participatory research project aimed at understanding current risk factors for obesity, diabetes, and cardiovascular disease in Alaska Natives living in Southwest Alaska. We utilize a multidisciplinary approach that includes assessment of genetic, nutritional and behavioral risk factors and their interrelationships with one another in the overall development of disease. The design of the CANHR project involved community participation in the development, implementation and interpretation of research results. We have developed a participatory research program that is designed to be culturally appropriate, relevant to community needs and interests, and respectful to our participants. This manuscript describes the organizational development of our CANHR study and the procedures employed in its progression to date.