Abstract. Wind farm sites within complex terrain are subject to local wind phenomena, which have a huge impact on a wind turbine's annual energy production. To reduce investment risk, an extensive site evaluation is therefore mandatory. Stationary long-term measurements are supplemented by CFD simulations, which are a commonly used tool to analyse and understand the three-dimensional wind flows above complex terrain. Though being under heavy research, such simulations still show a huge sensitivity for various input parameters like terrain, atmosphere and numerical setup. Within this paper, a different approach aims to measure instead of simulate wind speed deviations above complex terrain by using a flexible, airborne measurement system. An unmanned aerial vehicle is equipped with a standard ultrasonic anemometer. The uncertainty of the system is evaluated against stationary anemometer at different heights and shows very good agreement, especially in mean wind speed (