The temperature regime of alpine permafrost is altered by the generally warmer atmospheric temperatures of recent decades. Eight boreholes, with depths between 100 and 130 m, have recently been drilled in European mountain permafrost as part of the Permafrost and Climate in Europe (PACE) project. They have been equipped with temperature sensors in order to better understand and quantify the effect of climate change on permafrost temperatures. Their interpretation with respect to signals of surface temperature histories is complicated by topographic effects. An apparent warming signal is present in all of the PACE boreholes but quantification of this effect in mountainous terrain remains difficult. The influence of topography and spatially-variable surface temperatures on temperature-depth profiles is demonstrated with measurements from the Stockhorn borehole and a simple model. A conceptual framework for the interpretation of topographically-disturbed temperature-depth profiles and the modelling of temperature histories based on these data is proposed.