Radioactive waste disposal and management presents a unique problem at the Krško nuclear power plant as it is built and co-owned by the Republic of Croatia and the Republic of Slovenia. Each country is responsible for the management of half of the low-and intermediate-level radioactive waste (LILW) and spent nuclear fuel (SNF). So far, Slovenia has officially selected the site for LILW disposal and the Croatian programme has a single location left (since 1999), not officially approved as acceptable. This paper contains a new approach to site selection related to the implementation of GIS technology and presents a map of potential areas for LILW disposal including only the remaining Croatian location. It was constructed based on eleven layers that include natural characteristics and anthropogenic pressures. For the construction of the main map, detailed topological checks and spatial analysis of polygons have been made, reducing potential areas to be further evaluated.