The paper analyses the challenges posed to the principle of academic autonomy by the knowledge society and new conceptions of the state. It argues that these signify the breaking down of boundaries that have been critical for the justification of academic rights to self-government and freedom of inquiry. The ideal of academe as a sovereign, bounded territory, free by right from intervention in its governance of knowledge development and transmission, has been superseded by ideals of engagement with societies in which academic institutions are "axial structures". The paper then explores alternative concepts of institutional and individual self-determination within a reconfigured polity, in which boundaries are permeable and the governance of knowledge and knowledge-based institutions is shared and often contested between the state, the market and academic institutions. Institutional and individual academic autonomy understood in this way is not given or achieved once and for all, but neither is it out of academic control. (Contains 2 notes.)