Using an atmospheric inversion model we investigate the southern hemisphere ocean CO2 uptake. From sensitivity studies that varied both the initial ocean flux distribution and the atmospheric data used in the inversion, our inversion predicted a total (ocean and land) uptake of 1.65–1.90 Gt C yr−1. We assess the consistency between the mean southern hemisphere ocean uptake predicted by an atmospheric inversion model for the 1991–1997 period and the T99 ocean flux estimate based on observed ΔpCO2 in Takahashi et al. (2002; Deep-Sea Res II, 49, 1601–1622). The inversion can not match the large 1.8 Gt C yr−1 southern extratropical (20–90°S) uptake of the T99 ocean flux estimate without producing either unreasonable land fluxes in the southern mid-latitudes or by increasing the mismatches between observed and simulated atmospheric CO2 data. The southern extratropical uptake is redistributed between the mid and high latitudes. Our results suggest that the T99 estimate of the Southern Ocean uptake south of 50°S is too large, and that the discrepancy reflects the inadequate representation of wintertime conditions in the T99 estimate.