Amyotrophic lateral sclerosis (ALS) is a progressive, lethal neurodegenerative disease that selectively affects motor neurons. Reactive oxygen species (ROS) are assumed to be involved in the pathogenesis of ALS. Metallothioneins (MTs) are self-protective, multifunctional proteins that scavenge ROS. In particular, metallothionein-III (MT-III) has a strong scavenging effect on hydroxyl radicals. MTs have been suggested to have important roles in the pathophysiology of ALS. Therefore we investigated single nucleotide polymorphisms (SNPs) of the MT-III and the metallothionein-IIA (MT-IIA) promoter region in 37 Japanese SALS cases and 206 sex-matched healthy controls using polymerase chain reaction (PCR)-direct sequencing or PCR-temporal temperature gradient gel electrophoresis (TTGE). We detected no SNPs of the MT-III gene in SALS cases and controls, and no detectable association between SALS phenotypes and a SNP of the MT-IIA promoter region. We conclude that gene polymorphisms of MT-IIA promoter region and MT-III gene are not associated with SALS phenotypes in a Japanese population.