At 2 and 4 weeks following treatment with phenobarbital (PB), the classical nongenotoxic rodent liver carcinogen, we elucidated unique gene expression changes (both induction and repression) in liver tumor-susceptible B6C3F1 mice, as compared with the relatively resistant C57BL/6. Based on their cancer-related roles, we believe that altered expression of at least some of these genes might underlie PB-induced liver tumorigenesis. Putative constitutive active/androstane (CAR) response elements (CAREs), a subset of PB response elements, were present within multiple genes whose expression was uniquely altered in the B6C3F1 mice, suggesting a role for CAR in their regulation. Additionally, three DNA methyltransferase genes (Dnmt1, Dnmt3a, and Dnmt3b) were repressed uniquely in the tumor-prone B6C3F1 mice, and all possess putative CAREs, providing a potential direct link between PB and expression of key genes that regulate DNA methylation status. Previously, we demonstrated that PB-elicited unique regions of altered methylation (RAMs) in B6C3F1 mice, as compared with the relatively resistant C57BL/6, at 2 and 4 weeks, and annotation of the regions harboring these changes revealed 51 genes. This is extended by the current study, which employed RNA isolated from the same liver tissue used in the earlier investigations. Genes elucidated from both the methylation and expression analyses are involved in identical processes/pathways (e.g., cell cycle, apoptosis, angiogenesis, epithelial-mesenchymal cell transition, invasion/metastasis, and mitogen-activated protein kinase, transforming growth factor-beta, and Wnt signaling). Therefore, these changes might represent very early events that directly contribute to PB-induced tumorigenesis. It is instructive to consider the possibility that, in a hypothesis-driven fashion, these genes are initial candidates that could be utilized to develop a biomarker "fingerprint" of early exposure to PB and PB-like compounds.