The authors set out to study the role of T1-weighted muscle MRI in the diagnostic phase of ALS, comparing images from ten patients and nine age-matched healthy controls (HCs). All subjects underwent MRI of 68 muscles in the hands, paraspinal regions and lower limbs; the images were semi-quantitatively scored. Atrophy was more frequent in muscles of ALS patients than HCs (p < 0.0001); fatty infiltration was particularly marked in iliopsoas (p = 0.046), anterior (p = 0.020) and posterior (p = 0.047) calf muscles in patients. A trend towards agreement was found between MRI and clinic-EMG data for the first dorsal interosseous, paraspinal, and tibial anterior muscles. Muscle T1-weighted MRI can distinguish ALS patients from HCs for specific regions (i.e., legs). MRI abnormalities could be found in pauci-symptomatic spinal muscles in bulbar-onset patients. Muscle MRI may be a useful diagnostic tool in ALS, in particular for muscles difficult to investigate using clinical-EMG methods.