In the light of the shared features of intermediate length repeats and the pathological interaction of C9orf72 and ATXN2 genes in ALS pathogenesis, we performed the joint analyses of non-pathological repeats of C9orf72 (i.e., < 30) and intermediate repeats of ATXN2 (18–35) in 879 patients with ALS and 535 neurologically healthy controls, aiming to explore the risk of ALS and prognostic factors in ALS patients without C9orf72 HRE. Here, C9orf72 is linked to amyotrophic lateral sclerosis.