Profiles of wind speed and direction at high spatial and temporal resolution are fundamental meteorological quantities for studies of the atmospheric boundary layer. Ship-based Doppler lidar measurements can contribute to fill the data gap over oceans particularly in polar regions. In the present study a non-motion stabilized scanning Doppler lidar was operated on board of RV Polarstern in the Arctic (June 2014) and Antarctic (December–January 2015/2016). This is the first time that such a system measured on an icebreaker in the Antarctic. A method for a motion correction of the data in the post-processing is presented. The wind calculation is based on vertical azimuth display (VAD) scans with eight directions that pass a quality control. Additionally a method for an empirical signal-to-noise ratio (SNR) threshold is presented, which can be calculated for individual measurement setups. Lidar wind profiles are compared to total of about 120 radiosonde profiles and also to wind measurements of the ship. The performance of the lidar measurements in comparison with radio soundings shows generally small RMSD (bias) for wind speed of around 1 m s −1 (0.1 m s −1 ) and for wind direction of around 12° (6°). The postprocessing of the non-motion stabilized data shows a comparable good quality as studies with motion stabilized systems. Two case studies show that a flexible change of SNR can be beneficial for special situations. Further the studies reveal that short-lived Low-Level Jets in the atmospheric boundary layer can be captured by lidar measurements with a high temporal resolution in contrast to routine radio soundings. The present study shows that a non-motion stabilized Doppler lidar can be operated successfully on an icebreaker. It presents a processing chain including quality control tests and error quantification, which is useful for further measurement campaigns.