To increase our understanding of the carbon cycle, we compare regional estimates of CO2 flux variability for 1980–1998 from atmospheric CO2 inversions and from process-based models of the land (SLAVE and LPJ) and ocean (OPA and MIT). Over the land, the phase and amplitude of the different estimates agree well, especially at continental scale. Flux variations are predominantly controlled by El Niño events, with the exception of the post-Pinatubo period of the early 1990s. Differences between the two land models result mainly from the response of heterotrophic respiration to precipitation and temperature. The “Lloyd and Taylor” formulation of LPJ [Lloyd and Taylor, 1994] agrees better with the inverse estimates. Over the ocean, inversion and model results agree only in the equatorial Pacific and partly in the austral ocean. In the austral ocean, an increased CO2 sink is present in the inversion and OPA model, and results from increased stratification of the ocean. In the northern oceans, the inversions estimate large flux variations in line with time-series observations of the subtropical Atlantic, but not supported by the two model estimates, thus suggesting that the CO2 variability from high-latitude oceans needs further investigation.