Specific neurological impairments in multiple sclerosis (MS) are dependent on the pathology in clinically eloquent areas of the central nervous system. We aimed to use diffusion tensor fiber tracking to identify the pyramidal tracts and corpus callosum in MS patients, measure the apparent diffusivity within the tracts, and evaluate whether this would correlate with relevant disability scores. Dual-echo and diffusion tensor magnetic resonance imaging (DT-MRI) brain scans were obtained from 29 patients with relapsing remitting MS, and 13 age and gender matched normal controls. Voxels from pyramidal tracts and corpus callosum were automatically identified using a tractography based algorithm. Mean apparent diffusion coefficient (ADC(av)) was measured for these tracts. Scores of Expanded Disability Status Scale (EDSS) and Paced Auditory Serial Addition Test (PASAT) were obtained. The median EDSS score was 2.5 (inter-quartile range 2-3.25). The ADC(av) in the pyramidal tracts (p=0.02) and corpus callosum (p=0.0004) in patients was significantly higher than in controls. Pyramidal tracts ADC(av) was correlated with pyramidal FSS (r=0.5, p=0.008). Corpus callosum ADC(av) was correlated with PASAT (r=-0.58, p=0.001). Global T2 lesion volume did not correlate with the EDSS, but correlated with ADC(av) of the pyramidal tracts (r=0.6, p=0.0007) and corpus callosum (r=0.8, p<0.0001). T2 lesion volume within the pyramidal tracts and corpus callosum correlated with ADC(av) in the pyramidal tracts (r=0.6, p=0.0009) and corpus callosum (r=0.65, p=0.0002) respectively, but not with pyramidal FSS or PASAT score. DT-MRI quantifies pathology in specific white matter tracts and may increase the specificity of MRI in monitoring progression of motor and cognitive deficits in MS.