This article examines the emergence of private universities in Meiji Japan (1868-1912). It begins by discussing the interrelationships of modernity projects with the emergence of state universities, and with the new state civil servants. Second, it reviews the processes through which forerunners of private universities emerged, considering academic freedom and political independence as linked in the thought of their founders. The third section offers case studies of Keio and Waseda Universities. Finally it explores the process of cultural transformation in four areas of social formation: how religion, gender, social stratification and political philosophy were affected by the state modernity projects and private universities' resistance. The conclusion summarises the combined effects of state and private universities. (Contains 92 footnotes.)