Diffusion tensor imaging (DTI) parameters such as mean diffusivity (MD) and fractional anisotropy (FA) assess aspects of structural integrity within tissue. In relapsing-remitting (RR) multiple sclerosis (MS), abnormalities in normal appearing brain tissue (NABT) have been shown cross-sectionally. The evolution of these abnormalities over time is unclear. We present a longitudinal study investigating early RR MS subjects. The aims were to determine DTI changes over two years and assess the potential of DTI as a longitudinal quantitative marker at this stage of MS. Fifteen controls and 28 patients with RR MS (median disease duration 1.9 years; median EDSS 1.5) had DTI yearly for two years. NABT and whole brain tissue (NABT plus lesions) FA and MD histograms analysed. At baseline, differences in FA were noted between patients and controls (mean [p = 0.042] and peak height [p = 0.008]), while at two years differences in MD were observed (mean [p = 0.008] and peak location [p = 0.024]). However there were no significant DTI differences in longitudinal rates of change between patients and cohorts. In conclusion, although subtle NABT abnormalities were detected in early RR MS, the absence of longitudinal change suggests a limited role for global DTI assessment of NABT in following the early disease course.