In this paper an approach, proposed in the frame of the IAEA International Project on Innovative Nuclear Reactors and Fuel Cycles (INPRO) and its Collaborative Project “Key indicators for innovative nuclear energy systems” (KIND) for a multi-criteria comparative assessment of different energy options was studied and applied. Comparative evaluation of two hypothetical energy systems - nuclear and non-nuclear was performed in the context of co-operation between small countries in the Balkan region. The evaluation was based on various criteria grouped into selected areas to cover different dimensions in terms of sustainability - economic, environment, public, safety, infrastructure. The results show that nuclear option obtained higher total scores and is thus the preferred option. The nuclear option performs better in the areas of economics, environment and national security and non-nuclear option has the advantage in areas of waste management, safety, public acceptance and infrastructure. The sensitivity and uncertainty analysis performed in the study enable to consider the impact of the input uncertainties on the ranking results and their stability. The study could be used to support decision makers in energy policy at national level, demonstrating the application of methodology.