The atmospheric CO2 and δ13C records for the last millennium have been analyzed to reconstruct the evolution and the temporal variability in the terrestrial and oceanic carbon sinks and to identify natural variations in the marine carbon cycle. Reconstructed natural variations in sinks are usually less than ± 0.2 Gt C yr−1 on time scales of decades to centuries and thus one order of magnitude smaller than the sink fluxes driven by the anthropogenic perturbation. The natural oceanic carbon cycle was generally close to steady state on a multi-decadal time scale. A large anomalous oceanic carbon sink is found around 1940 that is attributed to a higher than usual El Niño activity. Interannual variations in the oceanic sink as reconstructed for the 1980–1996 period are around ±1 Gt C yr−1 and are significantly correlated with the Southern Oscillation. The relatively low atmospheric CO2 concentrations between 1600 and 1750 were caused by an additional terrestrial storage of 40 Gt C. The land biota acted as a carbon source between 1750 and 1950 and as a sink afterwards. Terrestrial changes can be explained by land use emission up to 1920. Then, additional mechanisms such as CO2 fertilization are responsible for an estimated terrestrial sequestration of 100 Gt C between 1920 and 1996.