Current understanding of Williamite Scotland tends to emphasise a few familiar themes, especially Jacobitism, famine and the Darien scheme. This provides an opaque and arguably skewed view of the period and nowhere is that clearer than in Highland policy, where historiographical focus on the Jacobite rising and the massacre of Glencoe has come at the expense of a fuller understanding of how William's government responded to the perennial ‘Highland problem’. This article attempts to tackle that gap through analysis of Williamite Highland policy after 1692, with a particular emphasis on its major initiative, the Highland Judicial Commission of 1694. Reconstructing the development, structure, workings and intellectual underpinnings of the commission, both on its own terms and in comparison to the earlier commission of the 1680s upon which it was based, it is argued that William's government emerged as a more authoritarian, domineering presence in the Highlands than its immediate predecessors. This, in turn, has broader implications, not just in terms of questioning recent revisionism about the Williamite regime in Scotland, but also about the nature of peripheral control and state formation in the early modern period.