In the present study, we characterized the physiological aging of deep grey matter nuclei by simultaneously measuring quantitative magnetic resonance parameters sensitive to complementary tissue characteristics (volume atrophy, iron deposition, microstructural damage) in seven different structures in 100 healthy subjects. Large age-related variations were observed in the thalamus, putamen and caudate. No significant correlations with age were observed in the hippocampus, amygdala, pallidum, or accumbens. Multiple regression analyses of advanced imaging data revealed that the best predictors of physiological aging were the mean relaxation time (T2*) of the putamen and the volume and mean diffusivity of the thalamus. These three parameters accounted for over 70% of the age variance in a linear model comprising 100 healthy subjects, aged from 20 to 70 years. Importantly, the statistical analyses highlighted characteristic patterns of variation for the measurements in the various structures evaluated in this study. These findings contribute in establishing a baseline for comparison with pathological changes in the basal ganglia and thalamus.