At the turn of the century, American higher educational institutions were rapidly divesting themselves of their religious content and functions. The conscious attempt of the University of Illinois to separate itself from its fifty years of vaguely Protestant Christianity was representative of this process, which was, in fact, the final chapter in the gradual secularization of the higher learning that had prevailed in the Western European tradition for some eight hundred years. Fully to understand these developments entails a historical analysis of the complex and dialectical cultural and political changes that brought them about, including a critical definition of secularization as a way of thinking and as a social-political program. The practical problem, it is argued, is located in the post-Reformation tendency to confuse an institution of higher learning with a local church, the Yale experience furnishing an instructive example of this confusion. The result was a religious demand the university could not meet and a corresponding withdrawal of religion to a merely pastoral and psychological strategy in place of its former substantive intellectual role. Thanks to the “Kantian defense,” neither orthodoxy nor the new liberal Christianity (which might have been seen as a candidate to replace it in academe) any longer needed the university, both having retired to a safer autonomy. The resulting dilemma, that to be religious hampers learning, and that to be learned entails at least religious neutrality if not its complete abandonment, persists in present day conflicts over the role of religion in our educational institutions at all levels.