© Author(s) 2017. Location information from long-duration super-pressure balloons flying in the Southern Hemisphere lower stratosphere during 2014 as part of X Project Loon are used to assess the quality of a number of different reanalyses including National Centers for Environmental Prediction Climate Forecast System version 2 (NCEP-CFSv2), European Centre for Medium-Range Weather Forecasts (ERA-Interim), NASA Modern Era Retrospective-Analysis for Research and Applications (MERRA), and the recently released MERRA version 2. Balloon GPS location information is used to derive wind speeds which are then compared with values from the reanalyses interpolated to the balloon times and locations. All reanalysis data sets accurately describe the winds, with biases in zonal winds of less than 0.37 ms -1 and meridional biases of less than 0.08 ms -1 . The standard deviation on the differences between Loon and reanalyses zonal winds is latitude-dependent, ranging between 2.5 and 3.5 ms -1 , increasing equatorward. Comparisons between Loon trajectories and those calculated by applying a trajectory model to reanalysis wind fields show that MERRA-2 wind fields result in the most accurate simulated trajectories with a mean 5-day balloon-reanalysis trajectory separation of 621 km and median separation of 324 km showing significant improvements over MERRA version 1 and slightly outperforming ERA-Interim. The latitudinal structure of the trajectory statistics for all reanalyses displays marginally lower mean separations between 15 and 35° S than between 35 and 55° S, despite standard deviations in the wind differences increasing toward the equator. This is shown to be related to the distance travelled by the balloon playing a role in the separation statistics.