The purpose of this work is to evaluate the efficiency of the biggest commercial banks that operated in Greece at the financial year 2009. The method used is Data Envelopment Analysis. Each bank is modelled as a linear system with multiple inputs and outputs. The innovation of the paper refers to the choice of data and the use of a combination of the intermediation approach and the Sealey and Lindley (1977) approach. The data used was derived from the Hellenic Banks Association and from the balance sheets of its members. These data include the interest expenses, fixed assets, deposits etc. To estimate the relative efficiency of the chosen DMU’s the MS Excel add-in program xIDEA 2.1 is employed. The results indicate several inefficiencies that may not have direct relation to the profitability of such institutions. But, these inefficiencies indicate the vulnerability of the Greek banking system and its potential to ask for help from the FSF (Financial Stability Fund).