2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) is a potent rodent carcinogen and a potential human carcinogen because of its existence in the normal human diet. N2-OH-PhIP, a major PhIP metabolite, has been identified as a precursor of genotoxic species. In vitro data supported the view that CYP1A2 is the major enzyme responsible for the formation of N2-OH-PhIP. However, disruption of the CYP1A2 gene in mouse failed to inhibit PhIP-induced carcinogenesis. To investigate the mechanism underlying this observation, the metabolism of PhIP in wild-type, Cyp1a2-null, and CYP1A2-humanized mice was examined in detail using a metabolomic approach. Following data acquisition in a high-resolution LC-MS system, urinary metabolomes of the control and PhIP-treated mice were characterized in a principal component analysis (PCA) model. Comprehensive metabolite profiles of PhIP in high dose (10 mg/kg) and low dose (100 microg/kg) were established through analyzing urinary ions contributing to the separation of three mouse lines in the multivariate model and by measuring radiolabled PhIP metabolite in a radio-HPLC assay, respectively. The genotoxicity of PhIP to three mouse lines was evaluated by measuring DNA adduction levels in liver, lung, colon, and mammary gland. On the basis of the chemical identities of 17 urinary PhIP metabolites, including eight novel metabolites, multivariate data analysis revealed the role of CYP1A2 in PhIP metabolism and a human-mouse interspecies difference in the catalytic activity of CYP1A2. In addition, the results also showed that Cyp1a2-null mice still possess significant N2-hydroxylation and DNA adduction activities, which may be partially attributed to mouse CYP2C enzymes according to the results from in vitro microsome and Supersome incubations and antibody inhibition experiments.