Conventional magnetic resonance imaging (MRI) measures of multiple sclerosis patients provide limited information about the nature and the extent of brain damage and repair. We established a clinically compatible protocol including quantitative MRI techniques (qMRI, T1, T2, T2* relaxometry) and semiquantitative Magnetisation Transfer Imaging to provide a comprehensive MRI fingerprint (CMF) of lesions that is more adherent to the real underlying pathology and to assess the CMF contribution to clinical performances in patients. Lesions characteristics, revealed by combination of q/sq MRI, highly correlated with patients clinical performance and more severe lesions appeared to drive the clinic-radiological correlations.