This dissertation interrogates the relationship between intellectuals and the state in the late nineteenth and early twentieth centuries in Chile, Mexico and Brazil. I use the term incomplete secularization to describe part of a process under which positivism, as one of the predominant discourses of the turn of the century milieu, deployed an ambitious plan for the institutional installation of a Positivist Church. The Positivist Church's distinctive feature was that it never laid claim to state bureaucracy, choosing instead to construct a parallel institution of its own that would tend to the final dissolution of the state itself. I argue that an examination of the roots and conditions of the emergence of the Positivist Church in both countries can help us to better understand this moment, in which the complex autonomy of the state was paradoxically premised on the incomplete process of secularization. The Positivist Church claimed that the way to close the gap between "the death of God" and the scientific and industrial revolutions was to create an institution that absorbed the structure of the Catholic Church but at the same time recognized the advances of Western philosophy and the sciences. I contend that the failure of the Positivist Church's intervention into the secularization process within the broader intellectual history of the period can illuminate the failure of the process of state constitution itself.