BACKGROUND : Relapsing-Remitting MS (RRMS) Deep Grey Matter (DGM) 5 year changes were examined using MRI measures of volume, transverse relaxation rate (R2*) and quantitative magnetic susceptibility (QS). By applying Discriminative Analysis of Regional Evolution (DARE), R2* and QS changes from iron and non-iron sources were separated. METHODS : 25 RRMS and 25 age-matched control subjects were studied at baseline and 5-year follow-up. Bulk DGM mean R2* and QS of the caudate nucleus, putamen, thalamus and globus pallidus were analyzed using mixed factorial analysis (α = 0.05) with sex as a covariate, while DARE employed non-parametric analysis to study regional changes. Regression/correlation analysis was performed with disease duration and MS Severity Score (MSSS). RESULTS : No significant change in Extended Disability Status Score was found over 5 years (baseline = 2.4 ± 1.2; follow-up = 2.8 ± 1.3). Significant time effects were found for R2* in the caudate (Q = 0.000008; η2 = 0.36), putamen (Q = 0.0000007; η2 = 0.43), and globus pallidus (Q = 0.0000007; η2 = 0.43), while significant longitudinal effects were only found for QS in the putamen (Q = 0.002; η2 = 0.22). Significant bulk interaction was only found for thalamus volume (Q = 0.02; η2 = 0.20). Iron decrease was the only detected significant effect using DARE, and the highest significant DARE effect size was mean thalamus R2* iron decrease (Q = 0.002; η2 = 0.26). No significant correlations or regressions were demonstrated with clinical measures. CONCLUSIONS : Thalamic atrophy was the only bulk effect that demonstrated different rates of changes over 5 years compared to age-matched controls. DARE Iron decrease in regions of the caudate, putamen, and thalamus were prominent features in stable RRMS over 5 years.