Medical geography and medical cartography can be denoted as classical application domains for Geographical Information Systems (GISs). GISs can be applied to retrospective analysis (e.g., human population health analysis, medical infrastructure development and availability assessment, etc.), and to operative disaster detection and management (e.g., monitoring of epidemics development and infectious diseases spread). Nevertheless, GISs still not a daily-used instrument of medical administrations, especially on the city and municipality scales. In different regions of the world situation varies, however in general case GIS-based medical data accounting and management is the object of interest for researchers and national administrations operated on global and national scales. Our study is focused onto the investigation and design of the methodology and software prototype for GIS-based support of medical administration and planning on a city scale when accounting and controlling infectious diseases. The study area is the administrative territory of the St. Petersburg (Russia). The study is based upon the medical statistics data and data collection system of the St. Petersburg city. All the medical data used in the study are impersonalized accordingly to the Russian laws.