Nanosized Co clusters (of about 3 nm size) were unambiguously identified in Co-doped ZnO thin films by atom probe tomography. These clusters are directly correlated to the superparamagnetic relaxation observed by ZFC/FC magnetization measurements. These analyses provide strong evidence that the room-temperature ferromagnetism observed in the magnetization curves cannot be attributed to the observed Co clusters. Because there is no experimental evidence of the presence of other secondary phases, our results reinforce the assumption of a defect-induced ferromagnetism in Co-doped ZnO diluted magnetic semiconductors.