In this paper, patterns of allelic imbalances (AIs) in chemically induced rat mammary, colon, and bladder tumors from (Wistar Furth x Fischer 344)F1 rats are described and compared. Male F1 rats were administered azoxymethane (AOM), and colon tumors were collected at 58 wk after treatment. Female F1 rats were given either N-nitroso-N-methylurea (NMU) or N-butyl- (hydroxybutyl)-nitrosoamine (BBN), and mammary and bladder tumors were collected at 15 and 52 wk after treatment, respectively. DNA was extracted from a subset of 18 of the largest tumors from each group, and a genome scan was performed by using polymerase chain reaction and 90 polymorphic microsatellite markers. AIs, such as loss of heterozygosity, gene duplication, and microsatellite instability, were observed at low frequencies in all of the tumor models. Thirty random AIs were observed in the AOM- induced colon tumors but only four in the NMU-induced mammary tumors. In both these models, all the tumors were classified as adenocarcinomas, and most of the AIs observed were confined to single tumors with atypical histopathology. In contrast, 27 random AIs were identified in the BBN-induced bladder tumors. AIs were observed in both transitional-cell carcinomas and papillomas, although most were in the carcinomas. Statistical analysis of the AI data revealed no significant nonrandom AIs within or among the tumor models, although several of the infrequently observed AI events identified in the rat tumors may also be observed in the corresponding human tumor type.