Susceptibility-weighted imaging (SWI) was developed as a diagnostic tool for amyotrophic lateral sclerosis (ALS). However, its sensitivity and specificity are insufficient for accurate diagnosis. Herein, we investigated a new, simple evaluation method for SWI as a diagnostic marker for ALS. We retrospectively investigated 36 patients with ALS and 19 healthy controls. The low signal intensity was semi-quantitatively evaluated on SWI using the motor cortex low intensity (MCLI) score: the sum score of the visual evaluation for the signal intensity of the bilateral primary motor cortices (orofacial, upper-limb, and lower-limb regions) from 0 (isointense) to 2 (markedly hypointense) with a total of 12 points. The mean MCLI score of two independent raters was significantly higher in ALS (median [interquartile range]; 5 [4-6]) than in controls (0 [0-1]), p < 0.0001. When the cutoff value of the MCLI score was set to 3, the area under the receiver operating characteristic curve was 0.973, and the sensitivity and specificity were 0.92 and 1.00, respectively. The MCLI score was not significantly correlated with age, disease duration, and ALS functional rating scale-revised (FRS-R), but was significantly correlated with the progression rate (∆FRS) (ρ = 0.39, p = 0.021) and upper motor neuron score (ρ = 0.51, p = 0.0014). Therefore, MCLI scoring is a useful diagnostic marker for ALS as the MCLI score was correlated with the UMN and ∆FRS scores.