The molecular mechanisms leading to gallbladder carcinoma (GBC) are poorly understood. Different molecular disorders, including nuclear and mitochondrial genomic alteration, are associated with different cancers. The frequency of mitochondrial genome mutation has remained completely unexplored. In GBC, this is the first report of a mutation analysis in the mitochondrial genome, especially in the D-loop region. For a comprehensive D-loop view in GBC in humans, we sequenced the mitochondrial genome of 35 GBC patients and matched germ-line DNA. A wide range of point mutations and polymorphisms was observed. These variations in the D-loop sequence of human GBC represent good evidence of the mitochondrial role in GB carcinogenesis and may be used as a marker for GBC.