Previous analyses by Levitus et al.  (“Levitus”) of ocean temperature data have shown that ocean heat content has increased over the last fifty years with substantial temporal variability superimposed. The HadCM3 coupled atmosphere–ocean general circulation model (AOGCM) simulates the Levitus trend if both natural and anthropogenic forcings are included. In the relatively well-observed northern hemisphere upper ocean, HadCM3 has similar temporal variability to Levitus but, like other AOGCMs, it has generally less variability than Levitus for the world ocean. We analyse the causes of this discrepancy, which could result from deficiencies in either the model or the observational dataset. A substantial contribution to the Levitus variability comes from a strong maximum around 500 m depth, absent in HadCM3. We demonstrate a possibly large sensitivity to the method of filling in the observational dataset outside the well-observed region, and advocate caution in using it to assess AOGCM heat content changes.