The paper describes the process of modeling functional structure of a geographically distributed commercial medical organization, based on a case of specific medical organization in Russian Federation. Based on the reference model of a commercial medical organization functional structure the main, management and supporting functions were analyzed. Based on the analysis and using the Archi enterprise architecture tool the functional structure taking into account the issue of geographical distribution was developed. The result of the research can be used as a starting point for developing a system of business processes as well as information requirements of the geographically distributed commercial medical organization.