New magnetic resonance (MR) measures considered to be putative workers of demyelination and axonal loss were found to be more closely related to clinical disability than T2-weighted MR imaging (MRI) findings in patients with multiple sclerosis (MS). In this study, we evaluated the reproducibility of such measurements in order to assess their reliability for longitudinal studies in MS. The intra-observer coefficients of variation for repeated measurements did not significantly differ among the MR techniques studied [2.6% for T2-weighted MR, 4.38% for unenhanced T1-weighted MRI, 3.65% for magnetisation transfer imaging (MTI) and 2.28% for spinal cord cross-sectional area at C5]. Our findings suggest that non-conventional MR techniques may be reliable outcome measures for clinical trials in MS.