Uncertainty estimation for Global Navigation Satellite System (GNSS) radio occultation (RO) soundings in the planetary boundary layer (PBL) depends on the algorithms used to process the RO data. We compare the refractivity retrievals from three RO processing centers – each with their own retrieval algorithm – in the PBL, finding a strong underestimation of refractivity in regions with the strongest refractivity gradients, especially in Jet Propulsion Laboratory (JPL) processing, as well as areas of weak overestimation of refractivity near the poles.