The lengthy history of interdisciplinary activity in higher education offers important lessons about developing, administering, and assessing interdisciplinary programs. A deepening body of literature surrounding higher education studies and organizational theory surrounds these lessons. This literature acknowledges that, like any other system, higher education institutions face multiple influences from both internal and external stakeholders. This interaction requires an understanding of the environment in which higher education institutions operate. This chapter begins from the position of a changing environment for higher education to consider the challenges associated with administering interdisciplinary programs. After establishing organizational norms unique to higher education institutions, the chapter considers three specific areas: (1) the role of boundaries in shaping the university, and how interdisciplinary programs negotiate these boundaries; (2) the persistence of disciplinary cultures, and their impact on interdisciplinary programs; and (3) the resource challenge for contemporary higher education, and how this debate affects interdisciplinary activities.