In order to disclose the relationship between mutations of mitochondrial DNA (mtDNA) and gastric carcinogenesis, we screened the entire mtDNA sequence in 30 cases of human gastric cancer and matched normal tissues by using denaturing high-performance liquid chromatography (DHPLC) and DNA sequencing. Our data showed that high frequency (66.7%, 20/30) of mitochondrial genome mutation occur red in gastric cancer. Among these variants, 17 cases (56.7%, 17/30) were identified to be somatic mutation. High level mutant frequency was found in ND4, ND5 c oding genes and D-loop control region, which was 36.7%, 26.7% and 30% respective ly. Comparing with complexes Ⅲ, Ⅳ and Ⅴof the electron transport chain, we found that variants appeared to be more frequent in the subunit genes of complexⅠ . Most of mutations were base substitutions (85.4%, 41/48). Our results suggested that mutations of subunit genes encoding complex Ⅰ, especially ND3, ND4 and N D5 genes, might contribute to human gastric carcinogenesis.