Annotation: Geographic information systems are increasingly being used in the military sphere and allow a new approach of collecting, processing, displaying and disseminating spatial information, data and knowledge of the territory for effective using in solving military-application problems related to inventory, analysis, modeling, forecasting and management of troops in the context of military operations. This feature stipulates the necessity of processing, not only geographic information, but also operational information, the main component, which is intelligence information. The addition of operational information to the geographic information systems, as a separate component, leads to increased computational complexity and a decrease in their efficiency. In order to increase the efficiency of the application of special-purpose geoinformation systems, reducing computing complexity and creating application software, the author of this article carried out a comparative analysis of the methods of handling various types of intelligence information in geoinformation systems of special purpose. This article uses the basic provisions of the theory of fuzzy sets, factor analysis, the theory of expert systems, neural networks, artificial intelligence, chaotic time series, spectral analysis methods, and others. According to the results of the comparative analysis of the methods of processing various types of intelligent information in geoinformation systems of special purpose, it has been established, that the most expedient method for obtaining an integrated assessment, based on the analysis of factors presented in numerical and verbal form is to use the method of the theory of fuzzy sets and fuzzy output. The direction of further research should be considered the development of a methodology for processing various types of intelligence information in special-purpose geoinformation systems and the development of a method for configuring the knowledge bases of modern information systems for processing various types of intelligence information in special-purpose geographic information systems, based on a genetic algorithm.