This article compares the temperature, zonal, and meridional velocities issued by the 50-year National Centers for Environmental Prediction–National Center for Atmospheric Research (NCEP-NCAR) Reanalysis (NN50) and European Centre for Medium-range Weather Forecasts (ECMWF) operational analyses with independent observations collected during the Vorcore superpressure balloon campaign. The ECMWF analyses are found to be more accurate than the NN50 reanalyses. In particular, an overall warm bias in the polar Southern Hemisphere lower stratosphere is found in NN50 (+1.51 K), while a cold bias is found using ECMWF analyses (−0.42 K). The ECMWF temperature bias evolves from winter (−1.34 K in September) to summer (+0.31 K in January). A common feature of both analyses is the localization of larger discrepancies with respect to the observations for all variables over the Antarctic Peninsula, where orographic gravity waves were observed. More generally, two principal reasons are put forth for explaining the reported differences with the observations: unresolved small-scale pure and inertia gravity waves affecting both analyses and a large-scale misrepresentation of the vortex in NN50. Finally, simulated trajectories are computed starting from the positions of the balloon and advected using the ECMWF and the NN50 velocity fields. The simulated trajectories are compared to the real balloon trajectories. The spherical distance between the real and simulated positions exceeds 1000 ± 700 km on average in just 5 days using NN50 and after 10 days using ECMWF. The distances between the simulated and real balloons are found to increase faster in November and December, owing to the strong Rossby-wave activity in the stratosphere.