A multivariate analysis of the upper ocean thermal structure is used to examine the recent long-term changes and decadal variability in the upper ocean heat content as represented by model-based ocean reanalyses and a model-independent objective analysis. The three variables used are the mean temperature above the 14°C isotherm, its depth and a fixed depth mean temperature (250 m mean temperature). The mean temperature above the 14°C isotherm is a convenient, albeit simple, way to isolate thermodynamical changes by filtering out dynamical changes related to thermocline vertical displacements. The global upper ocean observations and reanalyses exhibit very similar warming trends (0.045°C per decade) over the period 1965–2005, superimposed with marked decadal variability in the 1970s and 1980s. The spatial patterns of the regression between indices (representative of anthropogenic changes and known modes of internal decadal variability), and the three variables associated with the ocean heat content are used as fingerprint to separate out the different contributions. The choice of variables provides information about the local heat absorption, vertical distribution and horizontal redistribution of heat, this latter being suggestive of changes in ocean circulation. The discrepancy between the objective analysis and the reanalyses, as well as the spread among the different reanalyses, are used as a simple estimate of ocean state uncertainties. Two robust findings result from this analysis: (1) the signature of anthropogenic changes is qualitatively different from those of the internal decadal variability associated to the Pacific Interdecadal Oscillation and the Atlantic Meridional Oscillation, and (2) the anthropogenic changes in ocean heat content do not only consist of local heat absorption, but are likely related with changes in the ocean circulation, with a clear shallowing of the tropical thermocline in the Pacific and Indian oceans.