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By employing non-parametric methods, namely Data Envelopment Analysis and Malmquist Index, this paper investigates efficiency of banks using a database of almost all banks in four countries in South-East Europe. The superior efficiency of foreignowned banks in intermediation is supported. It is argued that the improvement in efficiency of banks originated from the change in technology rather than scale and technical efficiency, and banks on average have not been able to catch-up with best-performers, thus widening the efficiency gap. The largest sources of inefficiency are found to be cost and scale inefficiencies and lending shortfalls. Because of its peculiarities, Kosovo banking sector is assessed relative to other economies. Findings suggest that despite some improvements, the banking system in Kosovo remained less efficient. A number of policy implications emanate from the findings, aiming at enhancing the intermediation efficiency of banks in the context of South-East European transition.