Assessments of the state of health of Hindu-Kush–Karakoram–Himalaya glaciers and their contribution to regional hydrology and global sea-level rise suffer from a severe lack of observations1. The globally averaged mass balance of glaciers and ice caps is negative. An anomalous gain of mass has been suggested for the Karakoram glaciers but was not confirmed by recent estimates of mass balance. Furthermore, numerous glacier surges in the region that lead to changes in glacier length and velocity complicate the interpretation of the available observations. Here, we calculate the regional mass balance of glaciers in the central Karakoram between 1999 and 2008, based on the difference between two digital elevation models. We find a highly heterogeneous spatial pattern of changes in glacier elevation, which shows that ice thinning and ablation at high rates can occur on debris-covered glacier tongues. The regional mass balance is just positive at +0.11±0.22 m yr−1 water equivalent and in agreement with the observed reduction of river runoff that originates in this area. Our measurements confirm an anomalous mass balance in the Karakoram region and indicate that the contribution of Karakoram glaciers to sea-level rise was −0.01 mm yr−1 for the period from 1999 to 2008, 0.05 mm yr−1 lower than suggested before.