The correlation between T2 lesion load (LL) detected on conventional MR sequences and disability assessed by the Expanded Disability Status Scale (EDSS) in multiple sclerosis (MS) is, at best, moderate. The present study was performed to determine whether the correlation between disability and LL is improved by (i) use of the more sensitive three-dimensional fast fluid-attenuated inversion recovery (3D-fast FLAIR) sequence; (ii) application of the newly devised MS functional composite (MSFC) score. Forty-one patients with clinically definite or probable MS were studied. All had been followed prospectively for 14 years since their first symptom. EDSS and MSFC score were assessed. Imaging was performed with 3D-fFLAIR, fast spin-echo (FSE), and T1 weighted SE sequences. 3D-fFLAIR detected a 34% higher LL than FSE, but did not improve the correlation between T2 LL and EDSS (r = 0.51 and r = 0.53); the correlation was stronger with T1 LL (r = 0.57). The MSFC score did not significantly correlate with T2 LL or T1 LL. The robust correlation in this cohort between T2 LL and EDSS may reflect the homogeneous disease duration and the wide spread of disability. This correlation was not improved by the increased detection of T2 lesions with the 3D-fFLAIR sequence. The stronger correlation between T1 LL with EDSS is consistent with the finding that this subgroup of lesions represent areas of more severe tissue damage. The MSFC score did not improve the clinico-radiological paradox that is found in MS, despite including information on cognitive function.