The purpose of this paper is to present comparative partial analysis of relative positioning deviations of GPS and GLONASS global navigation satellite systems in polar areas. This subject is of great interest for successful ship management, i.e. ship navigation in polar regions as areas of increased traffic. The paper analyses the positioning performance of global and regional navigation systems that are still in use today and continuously developing, all in order to increase the speed and accuracy of signal transmission to the final user for obtaining the most accurate position. In maritime navigation, an incorrect position can be very dangerous. Moreover, when it comes to oceans and navigation in polar regions, it can mean additional sailing time, additional fuel consumption and especially it could threaten the security of the ship and crew. This is the reason why continuous development of GNSS system is required and this development should follow improvement of SBAS system (Satellite Based Augmentation System), respectively WAAS (Wide Area Augmentation System) system for the area of United States, EGNOS (European Geostationary Navigation Overlay Service) system for European continent and other systems that today provide coverage of almost the entire globe with a quality signal. The approach to estimate the position errors was done by statistical analysis of a data sets containing records of the positioning solutions measured at the selected stations in the selected time period. To make statistical analysis, firstly was required on which the analysis will be preformed, and then the preparation of the data that was necessary. In order to be able to successfully preform statistical data processing, a quality sample had to be selected. After checking data availavility a test period of seven days was selected and the results of that test are presented in thethesis. In this paper it can be seen which factors influence the somewhat worse positioning of satellite systems in the polar regions compared to other parts of the Earth. Moreover, comparison research of a set of statistical data on the recorded positions of the GPS system and the GLONASS system was made from which we can conclude that the GPS system is somewhat more accurate than the GLONASS system.