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Rising emissions of anthropogenic greenhouse gases (GHG) have led to tropospheric warming and stratospheric cooling over recent decades. As a thermodynamic consequence, the troposphere has expanded and the rise of the tropopause, the boundary between the troposphere and stratosphere, has been suggested as one of the most robust fingerprints of anthropogenic climate change. Conversely, at altitudes above ∼55 km (in the mesosphere and thermosphere) observational and modeling evidence indicates a downward shift of the height of pressure levels or decreasing density at fixed altitudes. The layer in between, the stratosphere, has not been studied extensively with respect to changes of its global structure. Here we show that this atmospheric layer has contracted substantially over the last decades, and that the main driver for this are increasing concentrations of GHG. Using data from coupled chemistry-climate models we show that this trend will continue and the mean climatological thickness of the stratosphere will decrease by 1.3 km following representative concentration pathway 6.0 by 2080. We also demonstrate that the stratospheric contraction is not only a response to cooling, as changes in both tropopause and stratopause pressure contribute. Moreover, its short emergence time (less than 15 years) makes it a novel and independent indicator of GHG induced climate change.