Abstract Longitudinal valleys form first order topographic features in many mountain belts. They are commonly located along faults that separate tectonic zones with varying uplift histories. The Indus Valley of Ladakh, northern India, runs northwestwards following the boundary between the relatively undeformed Ladakh Batholith to the north–east and the folded and thrusted Zanskar mountains to the south–west. In this region the Shyok Valley, on the northern side of the batholith, approximately parallels the course of the Indus. This study investigates geomorphic variations in transverse catchments that drain the Ladakh Batholith, into the Indus and Shyok rivers. The batholith has been divided into three zones based on varying structural characteristics of its northeastern and southwestern boundaries. Morphometric analysis of 62 catchments that drain into the Indus and Shyok valleys was carried out using three digital datasets, and supported by field observations. Morphometric asymmetry is evident in the central zone where the Shyok valley is considered tectonically inactive, but the Indus Valley is bound by the northeastwardly thrusting Indus Molasse and the batholith. In this zone the catchments that drain into the Indus Valley are more numerous, shorter, thinner and have lower hypsometric integrals than those that drain into the Shyok. By linking these observations with the regional geology and thermochronological data it is proposed that high sediment discharge from the deformed Indus Molasse Indus Valley has progressively raised base levels in the Indus Valley and resulted in sediment blanketing of the opposing tectonically quiescent catchments that drain southwestwards off the batholith. The Indus Molasse thrust front has propagated at least 36 km towards the Ladakh Batholith over the last 20 Ma. Hence it is proposed that this long term asymmetric structural deformation and exhumation has forced the Indus longitudinal valley laterally into the Ladakh Batholith resulting in the morphometric asymmetry of its transverse catchments.