Abstract. The upper troposphere and lower stratosphere (UTLS) represents a transition region between the more dynamically active troposphere and more stably stratified stratosphere. The region is characterized by strong gradients in the distribution of long-lived tracers, whose representation in models is sensitive to discrepancies in transport. We evaluate the GEOS-Chem model in the UTLS using carbon dioxide (CO 2 ) and ozone (O 3 ) observations from the HIAPER (The High-Performance Instrumented Airborne Platform for Environmental Research) Pole-to-Pole Observations (HIPPO) campaign in March 2010. GEOS-Chem CO 2 /O 3 correlation suggests that there is a discrepancy in mixing across the tropopause in the model, which results in an overestimate of CO 2 and an underestimate of O 3 in the Arctic lower stratosphere. We assimilate stratospheric O 3 data from the Optical Spectrograph and InfraRed Imager System (OSIRIS) and use the assimilated O 3 fields together with the HIPPO CO 2 /O 3 correlations to obtain an adjustment to the modeled CO 2 profile in the Arctic UTLS (primarily between the 320 and 360 K isentropic surfaces). The HIPPOderived adjustment corresponds to a sink of 0.60 Pg C for March-August 2010 in the Arctic. Imposing this adjustment results in a reduction in the CO 2 sinks inferred from GOSAT observations for temperate North America, Europe, and tropical Asia of 19, 13, and 49 %, respectively. Conversely, the inversion increased the source of CO 2 from tropical South America by 23 %. We find that the model also underestimates CO 2 in the upper tropical and subtropical troposphere. Correcting for the underestimate in the model relative to HIPPO in the tropical upper troposphere leads to a reduction in the source from tropical South America by 77 %, and produces an estimated sink for tropical Asia that is only 19 % larger than the standard inversion (without the imposed source and sink). Globally, the inversion with the Arctic and tropical adjustment produces a sink of −6.64 Pg C, which is consistent with the estimate of −6.65 Pg C in the standard inversion. However, the standard inversion produces a stronger northern land sink by 0.98 Pg C to account for the CO 2 overestimate in the high-latitude UTLS, suggesting that this UTLS discrepancy can impact the latitudinal distribution of the inferred sources and sinks. We find that doubling the model resolution from 4 • × 5 • to 2 • × 2.5 • enhances the CO 2 vertical gradient in the high-latitude UTLS, and reduces the overestimate in CO 2 in the extratropical lower stratosphere. Our results illustrate that discrepancies in the CO 2 distribution in the UTLS can affect CO 2 flux inversions and suggest the need for more careful evaluation of model errors in the UTLS.