Introduction: Gray matter (GM) atrophy is common in multiple sclerosis (MS), but the relationship with white matter (WM) pathology is largely unknown. Some studies found a co-occurrence in specific systems, but a regional analysis across the brain in different clinical phenotypes is necessary to further understand the disease mechanism underlying GM atrophy in MS. Therefore, we investigated the association between regional GM atrophy and pathology in anatomically connected WM tracts. Methods: Conventional and diffusion tensor imaging was performed at 3T in 208 patients with long-standing MS and 60 healthy controls. Deep and cortical GM regions were segmented and quantified, and both lesion volumes and average normal appearing WM fractional anisotropy of their associated tracts were derived using an atlas obtained by probabilistic tractography in the controls. Linear regression was then performed to quantify the amount of regional GM atrophy that can be explained by WM pathology in the connected tract. Results: MS patients showed extensive deep and cortical GM atrophy. Cortical atrophy was particularly present in frontal and temporal regions. Pathology in connected WM tracts statistically explained both regional deep and cortical GM atrophy in relapsing-remitting (RR) patients, but only deep GM atrophy in secondary-progressive (SP) patients. Conclusion: In RRMS patients, both deep and cortical GM atrophy were associated with pathology in connected WM tracts. In SPMS patients, only regional deep GM atrophy could be explained by pathology in connected WM tracts. This suggests that in SPMS patients cortical GM atrophy and WM damage are (at least partly) independent disease processes.