When the university met its modern concept, the speed of the autonomy arguments have never slowed down. The study, handles the university autonomy through a wide perspective by giving a variety of examples from different countries and therefore gives the reader a chance to make comparison. Accordingly, in the first chapter, the concept, the history and the evolution of the university in the United States of America, Europe -predominantly Germany and Turkey is being examined, including the general character of the higher education and state systems of those countries. After discussed in the social reality, the university is being discussed as an institution and in an organizational way. In the second chapter, the concept of autonomy which is unclear is examined from a philosophical perspective. Afterwards, the concept of autonomy, the elements of autonomy and the supervision of the state is discussed in a legal context. In the third chapter, the relationship between the university and the state is discussed by mentioning the prominent models of universities throughout the world. Then, the higher education systems of Turkey and Germany are being examined by representing the changing ideas and by partially comparing to the higher education system of United States of America. In the last chapter, the relationship between the market and the university is discussed and the latest models of universities are mentioned as a result of this intervention between the university and market. The change in the higher education is considered with the social change by discussing the changing role of the university in a knowledge based economy. In this respect, various facts are put forward like the concept of university as the new public sphere and the new weapon of the culture wars or the new imperialism. The study puts forth the new concept of autonomy in the inadequate one dimensioned point of view of the economic analysis which has occurred in the recent higher education reforms and offers a new higher education system for Turkey by considering the concrete social conditions.