Mitochondrial DNA (mtDNA) somatic mutations have been identified in nearly all kinds of cancer during the past decade. Normally one need to determine the complete mtDNA sequences from both cancerous and normal tissues of the same patient to score the somatic mutation in cancer. In this study, we intended to explore a strategy to quickly identify somatic mutations in the entire mtDNA genome based on its phylogeny. The principal assumption for this strategy is that somatic mutations, as recently accumulated in cancerous tissue, have younger age and will be located in the terminal branches of mtDNA phylogenetic tree. In contrast, the haplogroup-specific variants, which appear as germline variants and have ancient age, will be located in the basal or intermediate-node branches of the tree, depending on their relative age. When the complete mtDNA sequence of the cancerous tissue is determined and is classified relative to the available mtDNA phylogeny, we only need to screen the variants that are located in the terminal branch in the paracancerous tissue or other normal tissue from the same patient to identify somatic mutations in cancer. We validated this strategy by using paired gastric cancer tissue and paracancerous tissue or blood from 10 Chinese patients (including one with gastric stromal tumor). A total of seven somatic mutations were identified in the cancerous tissues from four patients. Our result suggests that employing mtDNA phylogenetic knowledge facilitates rapid identification of mitochondrial genome somatic mutations in cancer. (C) 2011 Elsevier B.V. All rights reserved.