This novel study compared quantitative magnetic susceptibility signal of deep grey matter (DGM) structures in the MS brain. We evaluated the QSM metrics in selected deep grey matter regions in 5 RRMS patients and 9 matched HCs. The STI suite software package was used for QSM image reconstruction. Compared to a reference region in HCs, a significant susceptibility change was detected in most DGM regions showing statistically significant RRMS cohort differences. QSM metrics in caudate showed strong correlations with depression scores, while pallidum and thalamus correlated significantly with anxiety. While results are limited due to small numbers, they provide the opportunity for further investigation in larger cohorts and strengthen these preliminary results.