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This paper analyzes the banking sector's performance of the two former Yugoslavian republics, Slovenia and Bosnia and Herzegovina. This study is the first study examining the efficiency of banking sector of two countries. Countries have formed their banking systems, with their central banks as central and main monetary institutions. Performance of the banking sector of the two countries is being examined, taking into account that one country is a post war country, while other succeeds to join to European Union. It is determined using the data on return on assets (ROA) as indicator of profit, and return on equity (ROE) as an expression of rentability of banking sector, then compared to nonperforming loans (NPL) in order to foreseethe affect on future lending. Foreign direct investment is also being examined due to the large portion of it was initially made into banking sector. Financial health of the banking sector is analyzed by comparing deposits to loans figures, in several structural aspects. Based on data Slovenia’s banking sector has higher return on equity throughoutyears, therefore it is more profitable.On the other hand Bosnia and Herzegovina’s banking sector is more risk protected, since banks have higher adequate capital that offers protection against risk.