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This study examines the initial opposition to the National Covenant from the masters of the universities of St Andrews, Glasgow and Aberdeen in 1638. It has generally been assumed that opposition to the Covenant among the intellectual elite was confined to the Aberdeen Doctors. The resistance in universities, however, was much more extensive. Only Edinburgh University, located in Scotland's revolutionary centre, supported the covenanting movement from the outset. In elucidating the widespread nature of opposition in universities, this article draws on a corpus of previously overlooked manuscript and printed sources, especially pertaining to the covenanters' debates with intransigent faculties at St Andrews and Glasgow, before setting the Aberdeen Doctors' resistance within the context of this wider academic hostility to the covenanting movement over the course of 1638. Though the universities' resistance was by no means coordinated, it, nevertheless, represented a pressing concern as the covenanters pursued a national movement. In examining these early intellectual arguments against the Covenant, this article illuminates university masters' stark differences with the covenanters over the nature of kingly authority, church government and religious ceremony. Because the universities trained Scotland's ministry and magistracy, these intellectual disagreements had pressing consequences. Thus, far from a minor encumbrance to the covenanting movement in 1638 that resulted in the subscriptions of the masters of Glasgow and St Andrews and the purge of the Aberdeen Doctors, the universities' resistance to the Covenant proved foundational to the covenanters' subsequent aggressive supervision of higher education within the construction of their fledgling confessional state in the 1640s.