The geoontology principles of identifying the functional connectivity of all components of the socio-biological system have been used as the basis for developing a unified and scientifically rigorous methodology of preprocessing of epidemiological information and its preparation for further use. The specific features of epidemiological information are highlighted as well as the need for territorial linkage of the objects and situations under study in order to ensure the adequacy of management decisions. According to the principles of designing relational databases, an integrated epidemiological database has been generated, which includes the geographical coordinates of the objects and situations under study. Such a territorial linkage when implemented using GIS technologies provides a means of solving regional problems of estimating the probability of disease with due regard for the specific features of the location, which ensures competent and targeted work of the system of medical and environmental monitoring. The continually updated databases have been created and patented, which are compatible with ArcGIS and contain basic epidemiological data on the incidence of tick-borne encephalitis and tick-borne borreliosis, based on information received from hospitals in Irkutsk. For updating the integrated database with information on the occurrence of infections across landscapes, annual (since 2005) expeditions have been conducted in several key areas of Irkutsk oblast which are distinguished by landscape diversity, vector size, attendance and morbidity of the population. Ticks and their hosts are collected and analyzed for the presence of pathogens of natural focal infections. More than 25 thousand ticks were caught, whose infection with tick-borne encephalitis virus averaged 1.5 %. Visualization of epidemiological information used the methods of end-to-end geographical mapping of the territory, the logic of which formulates the principles of geoinformation mapping and naturally includes a natural territorial component.Keywords: data processing methods, geoontology, epidemiological database, geocoding, end-to-end mapping, monitoring of morbidity rate.