The DNA alkylating agent, azoxymethane (AOM), induces tumor formation in the distal colon of susceptible mice. Differential susceptibility to this colonotropic carcinogen has been well characterized in A/J (sensitive) and AKR/J (resistant) mice. However, the reasons underlying the differential response to AOM and the molecular mechanisms involved in colon tumor progression remain unclear. To address these issues, we used a cDNA microarray approach to determine time-related changes in gene expression patterns in A/J and AKR/J colons following carcinogen treatment. In the present study, mice were injected intraperitoneally with either AOM (10mg/kg body weight once a week for 6 weeks) or 0.9% NaCl solution (vehicle controls). Total RNA was isolated from the distal colons at 1, 4, and 24 weeks post-AOM exposure. RNA was reverse transcribed and cDNA samples labeled with Cy3 and Cy5 were hybridized to a glass chip containing 4608 mouse cDNA duplicate clones. The resulting mRNA expression levels were analyzed using GLEAMS 3.0, a Unix/Linux-based software program. Genes with more than twofold variations in expression levels were considered significant. Further clustering analysis was performed based on gene expression patterns at different time points using a novel adaptive centroid algorithm (ACA). Of the 4608 genes, 118 clustered into 11 significant groups that displayed similar and distinct expression patterns between the strains following carcinogen treatment. Nine clusters were selected for further analysis based on their divergence in response between A/J and AKR/J and their potential role in tumorigenesis. Overall, our data indicate time- and strain-specific genetic alterations during different stages of colon tumorigenesis following AOM treatment.