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Valleys are remarkably persistent features in many different tectonic settings, but the reasons for this persistence are rarely explored. Here, we examine the structural controls on valleys in the Cairngorms Mountains, Scotland, part of the passive margin of the eastern North Atlantic. We consider valleys at three scales: straths, glens and headwater valleys. The structural controls on valleys in and around the Cairngorm Granite pluton were examined on satellite and aerial photographs and by field survey. Topographic lineaments, including valleys, show no consistent orientation with joint sets or with sheets of microgranite and pegmatitic granite. In this granite landscape, jointing is not a first-order control on valley development. Instead, glens and headwater valleys align closely to quartz veins and linear alteration zones (LAZs). LAZs are zones of weakness in the granite pluton in which late-stage hydrothermal alteration and hydro-fracturing have greatly reduced rock mass strength and increased permeability. LAZs, which can be kilometres long and >700 m deep, are the dominant controls on the orientation of valleys in the Cairngorms. LAZs formed in the roof zone of the granite intrusion. Although the Cairngorm pluton was unroofed soon after emplacement, the presence of Old Red Sandstone (ORS) outliers in the terrain to the north and east indicates that the lower relief of the sub-ORS basement surface has been lowered by <500 m. Hence, the valley patterns in and around the Cairngorms have persisted through >1 km of vertical erosion and for 400 Myr. This valley persistence is a combined product of regionally low rates of basement exhumation and of the existence of LAZs in the Cairngorm pluton and sub-parallel Caledonide fractures in the surrounding terrain with depths that exceed 1 km. © 2016, The Author(s).