Thorough the history of Republic one of the most discussed topics in Turkey is the question of relationship between state and religion and religious education. The main reason of this is that while the great majority of population is Muslim the structure of the state is secular. For this reason, the issues of religious education have been discussed since the establishment of the Republic. The first higher religious education in Turkey began by opening of Faculty of Theology at Ankara in 1949 and then other higher religious education called “Higher Islamic Institutes” opened in various cities in Turkey followed. All higher religious institutions were transferred to faculties of theology in 1982 and these educational institutions continued in this way up to 1997. However, after 1997, called as 28 February Process, many serious problems were lived in higher religious education as lived other areas of religious education. While the number of students at faculties of theology decreased dramatically in 2004-2005 academic year, after that both the number of faculties of theology and their students’ number began to rise quickly. At the moment, there are more than 100 faculties of theology in the country and they register 17 thousands students at average annually. Although the numbers of faculties and students continue to increase, there are still some important problems concerning higher religious education. This article discusses these problems and gives some examples from the western countries and advocates the quality rather than quantitative. The article concludes some suggestions concerning faculties of theology in Turkey.