Inadequacy of ratio analysis and parametric methods when comparing educational institutions and failure to achieve success in determining the most effective institutions, decision makers have led to the use of the Data Envelopment Analysis (DEA) technique, in comparative efficiency measures between in educational institutions. Furthermore, the number of research activities focused on the efficiency analysis of foundation universities in Turkey is not sufficient. The aims of this study are a) to determine the efficiencies of the foundation universities by using DEA which is a performance measurement method for increasing the efficiency of educational institutions and to rank foundation universities with regard to efficiency values (b) to examine which universities use their inputs unproductively and produce their output inefficiently. In this study, the numbers of professor, associate professor, assistant professor, research assistants and total budget expenses are used as input variables, the numbers of undergraduate, graduate and graduated students, the number of projects, the number of international publications are used output variables for 33 foundation universities in Turkey for year of 2009-2010. According to results, it is seen that Sabanci and Bilkent Universities are super-efficient for the academic year 2009-2010. Istanbul Arel University is the most inefficient university in Turkey. The findings indicate that foundation universities in Ankara are first, foundation universities in Izmir are second and foundation universities in Istanbul are the last order with regard to efficiency values. Besides, the foundation universities established before 2000 are more efficient than the foundation universities established after 2000 in Turkey.