Background: Despite growing acceptance and implementation of geographic information systems (GIS) in the public health arena, its utility for clinical population management and coordination by leaders in a primary care clinical health setting has been neither fully realized nor evaluated. Methods: In a primary care network of clinics charged with caring for vulnerable urban communities, we used GIS to (1) integrate and analyze clinical (practice management) data and population (census) data and (2) generate distribution, service area, and population penetration maps of those clinics. We then conducted qualitative evaluations of the responses of primary care clinic leaders, administrators, and community board members to analytic mapping of their clinic and regional population data. Results: Practice management data were extracted, geocoded, and mapped to reveal variation between actual clinical service areas and the medically underserved areas for which these clinics received funding, which was surprising to center leaders. In addition, population penetration analyses were performed to depict patterns of utilization. Qualitative assessments of staff response to the process of mapping clinical and population data revealed enthusiastic engagement in the process, which led to enhanced community comprehension, new ideas about data use, and an array of applications to improve their clinical revenue. However, they also revealed barriers to further adoption, including time, expense, and technical expertise, which could limit the use of GIS and mapping unless economies of scale across clinics, the use of web technology, and the availability of dynamic mapping tools could be realized. Conclusions: Analytic mapping was enthusiastically received and practically applied in the primary care setting, and was readily comprehended by clinic leaders for innovative purposes. This is a tool of particular relevance amid primary care safety-net expansion and increased funding of health information technology diffusion in these settings, particularly if the hurdles of cost and technological expertise are overcome by harnessing new advances in web-based mapping technology.