The scarce studies on the molecular pathways involved in the pathogenesis of rectal cancer indicate that these may vary, at least in part, from those relevant for colon cancer. Mitochondrial DNA alterations have been described in several human cancers. We aimed to study D310, ND1 and ND5 microsatellite sequence alterations and nuclear microsatellite instability in a series of 38 rectal carcinomas as compared to a series of 25 sigmoid carcinomas. D310 sequence alterations were observed in 34.3% and 37.5% of rectal and sigmoid carcinomas, respectively, whereas ND1 mutations were present in 2.6% in RC and ND5 mutations were detected in 5.3% and 8% of rectal and sigmoid carcinomas, respectively. A trend toward an association between nuclear and mitochondrial microsatellite instability was observed in sigmoid but not in rectal cancers. In conclusion, mitochondrial genome alterations are common in both rectal and sigmoid carcinomas and may contribute to their pathogenesis.