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This article addresses the methodological issues of using GIS technology in the development of nosogeographic maps that reflect the medical and geographical position of the Republic of Karakalpakstan. In the process of doing research, the territorial differentiation of morbidity of the population of the Republic of Karakalpakstan was identified and the geographical features of their distribution were highlighted. Differences in the northern and southern regions of the Republic of Karakalpakstan are mentioned, and the reasons for this discrepancy are given. All data had been collected from the Ministry of Health care and Department of Statistics of the Republic of Karakalpakstan. The infant mortality rates and population are calculated separately by districts, and these data are compared across the country. A series of nosogeographic maps, showing the medical and geographic situation in the administrative districts of the Republic of Karakalpakstan, was developed in ArcGIS 10.1. Statistical, cartographic, comparative geography, extrapolation, epidemiological and other research methods were used in scientific and applied research. As a result of the research, a number of nosogeographic maps were created. Proposals and recommendations for improving the creation of nosogeographic maps were made using GIS technologies. We believe that these maps will help governments and medical authorities more effectively implement medical and other ecological activities and plan their future work.