Amyotrophic lateral sclerosis (ALS) is a progressive disorder involving the degeneration of motor neurons. ALS shares pathogenic characteristics and genetic risk factors with multiple system atrophy (MSA). Here we examine whether a variant of the COQ2 gene associated with MSA in Japanese is also associated with ALS in Han Chinese. The ligase detection reaction was used to measure the frequency of the V393A variant of COQ2 in 282 patients with ALS and 491 healthy controls. The ALS and control groups showed no significant differences in genotype frequencies (OR 1.298, 95 %CI 0.396-4.253, p = 0.666) or allele frequencies (OR 1.314, 95 %CI 0.403-4.286, p = 0.650) at the V393A locus of COQ2. We also conducted a meta-analysis and combined our data with the previous Japanese research, but still failed to detect an association between V393A and ALS. In conclusion, This case-control study shows no evidence for an association between ALS and the V393A variant of COQ2 in Han Chinese and together with the Japanese research suggests that this polymorphism may not be linked to the risk of ALS in East Asians in general.