The association between clinical outcomes and abnormal susceptibility-weighted imaging (SWI)-filtered phase, indicative of increased iron content, as well as atrophy, was investigated in the subcortical deep-gray matter (SDGM) of multiple sclerosis (MS) patients. 149 relapsing-remitting (RR) and 61 secondary-progressive (SP) MS patients underwent SWI on a 3T scanner. Mean phase of the abnormal phase tissue (MP-APT) and normalized volumes were determined for the total and region-specific SDGM structures. In an age- and gender-adjusted regression model, total SDGM volume was the strongest predictor of Expanded Disability Status Scale (EDSS) (beta = -.224, p<.001), followed by total SDGM MP-APT (beta = -.168, p <.019). This model accounted for 30.4% of the variance in EDSS. Only SDGM MP-APT added additional variance in predicting EDSS, compared to conventional MRI metrics. Caudate and red nucleus MP-APT and amygdala volume were associated with EDSS. Our findings suggest that disability in MS patients is associated better with SDGM pathology, as indicated by increased iron content and atrophy, than with lesion burden or white matter and cortical volumes.