To substantiate differences in magnetic resonance (MR) patterns in clinical subgroups of multiple sclerosis (MS), we analyzed T2-weighted MR images of a large regional population of MS patients (n = 188). The patients had already been classified according to recent consensus definitions regarding the clinical course of MS into relapsing-remitting (RR), secondary progressive (SP) or primary progressive (PP). Significant (p < 0.01; Spearman test) differences were present between RR and SP patients regarding total lesion load, size and location of lesions. RR and PP patients showed similar MR patterns. PP and SP patients differed in total lesion load, small and medium-sized lesions. The degree of atrophy was highest for SP patients. The clinical progression rate [Expanded Disability Status Scale (EDSS)/disease duration] was similar for various subgroups; the MR progression rate (total lesion score/disease duration) was significantly larger for SP than for PP patients. The lesions load disability quotient (total lesion load/EDSS) differed between RR and PP patients and also between SP and PP patients. In SP patients, the total lesion load correlated significantly (Spearman rank correlation coefficient of 0.52) with EDSS. We conclude that PP patients differ in MR abnormalities from SP patients, that PP and RR patients have similar MR abnormalities and that RR and SP patients are at a different end of the same spectrum of the disease. As the dynamics and clinical impact of MS lesions are different in the various clinical subgroups, they should be considered separately in clinical trials.