This chapter outlines a theoretical framework for the study of university systems derived from the systems theory of Luhmann and Parsons, supplemented by Gouldner’s critical theory. The five components of the argument are: (a) ideologies, in general, can be defined by their relative intellectualization, which allows ideas to become systematic and structured at the social level; (b) organized ideologies consist of meaningful combinations of distinctions and justifications, most significantly among powerful elites; (c) the distinction between science/ideology functions as the operative code of the university system by externalizing ‘ideology’ as a special, exogenous mode of justification lacking the self-grounded authority of ‘science’; (d) this operative code is distributed across and within disciplines and faculties, but it is ‘bundled’ at the level of the university as a whole; and (e) systematic ignorance of the science/ideology distinction justifies academic autonomy inside the university while also reinforcing the authority of professionals working outside the academy.