Zinc oxide (ZnO) nanorods grown by the low-temperature (90 °C) aqueous chemical method with different cobalt concentration within the synthesis solution (from 0% to 15%), are studied by electron paramagnetic resonance (EPR), just above the liquid helium temperature. The anisotropic spectra of substitutional Co2+ reveal a high crystalline quality and orientation of the NRs, as well as the probable presence of a secondary disordered phase of ZnO:Co. The analysis of the EPR spectra indicates that the disappearance of the paramagnetic native core-defect (CD) at
is correlated with the apparition of the Co2+ ions lines, suggesting a gradual neutralization of the former by the latter. We show that only a little amount of cobalt in the synthesis solution (about 0.2%) is necessary to suppress almost all these paramagnetic CDs. This gives insight in the experimentally observed improvement of the crystal quality of diluted ZnO:Co nanorods, as well as into the control of paramagnetic defects in ZnO nanostructures.