Abstract. Wind farm sites in complex terrain are subject to local wind phenomena, which have a relevant 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 computational fluid dynamics (CFD) simulations, which are a commonly used tool to analyse and understand the three-dimensional wind flow above complex terrain. Though under intensive research, such simulations still show a high sensitivity to various input parameters like terrain, atmosphere and numerical setup. In 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 in the system is evaluated against stationary anemometer data at different heights and shows very good agreement, especially in mean wind speed (< 0.12 m s−1) and mean direction (< 2.4∘) estimation. A test measurement was conducted above a forested and hilly site to analyse the spatial and temporal variability in the wind situation. A position-dependent difference in wind speed increase of up to 30 % compared to a stationary anemometer is detected.