The use of free, open Geographical Information System (GIS) source software in Malaysia has evolved rapidly in the recent years, from a generating map digitally into a set of methods with various applications. Free open GIS source software has been utilised in health management fields due to its cost factor and user-friendly feature. Therefore, a comparison of selected free, open GIS source software focusing on the distribution of tuberculosis (TB) cases is presented in this paper to examine their functions and technical usability for local spatial epidemiological applications of Sarawak, Malaysia. Three health-based free open GIS source software are selected in this comparative study i.e., gvSIG, GeoDa and MapWindows GIS. These software's are possible alternatives to the licenced software (ArcGIS). The functions and output of each software are analysed using mapping, spatial analysis, and online system visualization. The free GIS open-source software might not be able to compete with licenced software in terms of advanced analysis. However, for basic mapping and spatial analysis functions such as heatmap mapping and hotspot detection, free GIS open-source software is a sufficient choice, especially for non-genetic or non-computer-based users.