Academic freedom is widely accepted as the legitimating concept which separates the academic profession from other professions. Over the last fifty years the dramatic changes in American higher education—from enrollment growth, shifts in funding sources, disciplinary specialization and diversification of institutional missions—have each influenced how academic freedom is actualized on college and university campuses. This study traces the history of academic freedom in American higher education from the late 1950s through the present. It asks about the current status and conceptions of academic freedom in American higher education, it considers what has shaped and influenced the current status and conceptions of American higher education, and it seeks to illuminate how the present state of professional autonomy is better understood through historical discussions of academic freedom. An organizational taxonomy is presented to explain the complexities of the domains, agents, and threats to academic freedom. The analysis revealed that a volatile, but nevertheless still identifiable, state of academic freedom existed throughout this tumultuous period. Because of this constant state of challenge and tension, the autonomy of the professoriate, and therefore the autonomy of higher education, has suffered.