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Background: Selective neurodegeneration in Amyotrophic Lateral Sclerosis (ALS) affects the primary motor system. We aimed to understand the relationship between cortical degeneration and the desintegration of the related motor corticospinal tract (CST) by applying both Diffusion Tensor Imaging (DTI) and the multi-component driven equilibrium single pulse observation of T1 and T2 (mcDESPOT). Methods: ALS patients (n = 27) were recruited for the NiSALS (Neuroimaging Society in Amyotrophic Lateral Sclerosis) registry and underwent cerebral neuroimaging and quantitative MRI. Age/range matched healthy control subjects (n = 21) provided a comparative dataset. Data was acquired on a SIEMENS Verio 3T scanner. DTI: EPI sequence, diffusion scheme with two b/values (0/100), 64 diffusion directions and a resolution of 2 mm[and]3. Mean diffusivity (MD), axial (AD) and radial diffusivity (RD) and fractional anisotropy (FA) measures were calculated. mcDESPOT: isotropic 1.7 mm[and]3 whole-brain data; FLASH (TR: 5.9 ms, FA = [4, 5.3, 6.6, 8, 9.3, 12, 17.3, 24][degrees]), trueFISP (TR 5.6 ms; FA = [9.8, 13.1, 16.4, 19.7, 22.9, 29.5, 42.6, 59][degrees]) and inversion prepared FLASH (TR 5.7 ms, FA = 5[degrees], TI [450, 700] ms, PE 72). The relaxation measures T1 time and T2 time, myelin water fraction (MWF) and residence time (MRT) were retrieved. The corticospinal tract (CST) was generated as region-of-interest (ROI) by tractographic reconstruction (DSIstudio) and diffusion measures were acquired. The multicomponent relaxation characteristics and myelin water measures were retrieved (Deoni et al.) including T1/T2 time, MWF and MRT of individual tracts. Results: Higher MD (p < 0.01) and lower FA (p < 0.01) were found in ALS CST. Notably, RD revealed highly significant lower values in ALS CST (p 0.0013). Whereas the CST MWF in ALS patients was non-significantly lower than in controls we found significantly higher values in CST MRT in ALS (p < 0.01). Discussion: Motor system degeneration in ALS effects CST integrity reflected by changes MD, RD and FA. Whereas significant differences in MRT also reveals early alteration of myelin integrity, the relative myelin content measured by MWF was assumably not significantly different in ALS given the early observation at the time of disease diagnosis. Conclusion: Secondary WM tract degeneration occurs early in disease. Besides the loss of structural integrity early alterations of the myelin characteristics indicate changes of its composition.