Refinement of in vitro systems for predictive toxicology is important in order to develop high-throughput early toxicity screening assays and to minimize animal testing studies. This study assesses the ability of mouse Hepa-1c1c7 hepatoma cell model under differing culture conditions to predict in vivo estrogen-induced hepatic gene expression changes. Custom mouse cDNA microarrays were used to compare Hepa-1c1c7 temporal gene expression profiles treated with 10 nM 17β-estradiol (E2) in serum-free and charcoal-stripped serum supplemented media at 1, 2, 4, 8, 12, and 24 h. Stripped serum supplemented media increased the number gene expression changes and overall responsiveness likely due to the presence of serum factors supporting proliferation and mitochondrial activity. Data from both experiments were compared to a gene expression time course study examining the hepatic effects of 100 μg/kg 17α-ethynyl estradiol (EE) in C57BL/6 mice at 2, 4, 8, 12, 18, and 24 h. Only 18 genes overlapped between the serum-free and in vivo studies, whereas 238 genes were in common between Hepa-1c1c7 cells in stripped serum data and C57BL/6 liver samples. Stripped serum cultured cells exhibited E2-elicited gene expression changes associated with proliferation, cytoskeletal re-organization, cholesterol uptake and synthesis, increased fatty acid β-oxidation, and oxidative stress, which correlated with in vivo hepatic responses. These results demonstrate that E2 treatment of Hepa-1c1c7 cells in serum supplemented media modulate responses in selected pathways which appropriately model estrogen-elicited in vivo hepatic responses.