Mitochondrial (mt) DNA mutations have been described recently in different tumors, whereas similar studies focusing on bladder cancer are scarce. In an effort to understand the significance of mtDNA mutations in bladder cancer, we investigated the mtDNA alterations in both clinical human bladder cancer and in a carcinogen-induced rat bladder cancer model. Human bladder cancer tissues were obtained by radical cystectomy and transurethral resection of bladder tumors. Rat bladder tumors were induced in SD rats by treatment with N-butyl-N-(4-hydroxybutyl) nitrosamine in drinking water for 24-28 weeks. Genomic DNA was extracted from tumor specimens and microdissected normal bladder mucosae. Mitochondrial genes and D-loop region were amplified by PCR. The amplified PCR fragments were either cloned into plasmid vector or used for direct DNA sequencing. The results of DNA sequence revealed numerous point mutations in the non-coding D-loop region and different mtDNA genes in both human and rat bladder cancers. In addition, we also detected deletions of variable lengths in mononucleotide repeats in the D-loop region, ND2, ATPase 8 and COIII genes in human bladder cancer samples. Our results show that mtDNA exhibits a high rate of mutations in both human and rat bladder cancers. We also demonstrate that the repetitive sequences of mononucleotides within the mt genome are unstable and subjected to deletions. The high incidence of mtDNA mutations in bladder cancer suggests that mtDNA and mitochondria could play an important role in the process of carcinogenesis and also mtDNA could be valuable as a marker for early bladder cancer diagnosis.