We screened 92 Japanese patients with sporadic AD (clinically diagnosed: 72 cases; autopsy-confirmed: 20 cases) and 59 age-matched controls for mitochondrial polymorphisms previously reported to be associated with increased risk in Caucasian AD. The polymorphisms in tRNA(Gln) (nt. 4336), 16S rRNA (nt. 3196), and ND1 (nt. 3397) were not found in either in Japanese AD or age-matched controls. The frequencies of these polymorphisms in Japanese seems to be very rare if not absent, indicating that these three mutations are not likely to be genetic risk factors of Japanese AD. In the analysis of polymorphisms of 12S rRNA, however, we identified two novel mutations, an insertion of three cytosines and an A to G transition at nt. 856, which have not been described before. The insertion of three cytosines was observed in one of the 90 AD cases, but not in 59 normal controls. The A to G transition at nt. 856 was found in 2 of the 90 AD cases, but not in 59 normal controls. These results raise the possibility that the mutations in the 12S rRNA are genetic risk factors for AD in Japanese population.