This article is aimed at expanding and deepening knowledge in GIS analysis for medical professionals. Key task of described research is to elaborate a methodology of 3D mapping and visualization of the multiflat buildings in order to study most socially valuable diseases on the apartment scale in the St. Petersburg city. The use of this methodology allows to avoid the aggregation of geographical information within one building, and, on the other hand, allows to move from a general assessment of the prevalence of the disease to specific cases. In this case, the methodology is considered as primary health care support. The paper describes elaborated approach to detailed 3D mapping of multiple disease hotbeds in multiflat buildings. Main benefit of the proposed set of data processing and mapping techniques is the capability of apartment-scale connectivity evaluation of the hotbeds inside multiflat buildings.