An inflammatory state has been associated with the decreased clearance of multiple drugs via mRNA repression and activity inhibition of multiple cytochrome P450 enzymes (CYPs). This phenomenon disallows accurate assessment of the pharmacokinetics in humans and can lead to changes in drug efficacy and toxicity thresholds. This repression effect has been linked to the increased release of several cytokines, including TNFα, IL-2, and interferons. To understand the molecular pathways in the hepatocyte transcriptome upon exposure to inflammatory mediators, we investigated the effects of lipopolysaccharide (LPS) and two well-characterized cytokines, TNFα (proinflammatory) and IL-4 (both pro- and anti-inflammatory), on the global mRNA expression in human hepatocytes. First, naïve human hepatocytes from a panel of 8 donors were shown to express moderate levels of the IL-4, TNF, toll-like, and several other receptors. Subsequently, human hepatocytes plated in collagen coated plates were treated with IL-4, TNFα, or LPS for 48h. The RNA from these cells was then analyzed using whole human genome Affymetrix microarrays. The global gene expression profiles, revealing >3000 transcriptomic changes, were similar for LPS and TNFα treated hepatocytes, but remarkably distinct from the IL-4 treatments. In general, several major liver CYPs were repressed in all treatment groups, including CYP3A4 which was repressed to a lesser degree in IL-4 treated hepatocytes. CYP2E1 was induced only upon IL-4 exposure. Few transcripts (~40) were upregulated in common between all treatments with several of these being involved in cell adhesion, migration, and chemotaxis. Considerably more genes (~150) were downregulated similarly in all of the treatments, including GSTs, FMO3, UGTs, and transporters. The PXR xenosensor, a major regulator of CYP expression, was significantly repressed by all treatments. HNF4α, which also participates in the regulation of phase I enzymes, was significantly downregulated in the presence of TNFα and LPS, but not IL-4. Both LPS and TNFα treatments substantially enhanced the expression of secondary cytokines, such as MCP-1, IL-1, IL-6, and IL-8, but IL-4 treatment had little effect on the level of proinflammatory factors. Both LPS and TNFα, but not IL-4, significantly amplified the expression of multiple factors involved with toll-like receptor and NF-κB signaling. IL-4 had a significant repression on TGFβ and PDGF signaling with only minor changes observed with TNFα and LPS. IL-4 upregulated the expression of several cyclins, whereas TNFα and LPS repressed these factors. These data support the notion that TNFα and LPS are more proinflammatory compared to IL-4 in primary hepatocytes, and may contribute toward further understanding of the molecular interactions involved in phase I enzyme repression.