Objectives: With particular emphasis on interactions between cholesterol homeostasis and drug metabolism we investigate the global transcriptome of human primary hepatocytes treated by two commonly prescribed cholesterol lowering drugs atorvastatin and rosuvastatin and by rifampicin that serves as an outgroup as well as a model substance for induction of nuclear receptor PXR. Methods: Hepatocytes from human donors have been treated with rosuvastatin, atorvastatin and rifampicin for 12, 24 and 48h. Expression profiling with cholesterol and drug metabolism enriched low density Steroltalk cDNA and whole genome Affymetrix HG-U133 Plus 2.0 arrays has been applied. Differential expression of genes and gene set enrichment analysis of KEGG pathways were performed. Lists of differentially expressed genes and gene sets were cross-compared. Selected genes were confirmed by qPCR. Results: Statins lead to: (a) upregulation of cholesterol-related genes indicating increased LDL uptake and storage of esterified cholesterol, elevated bile acid/drug export and lower capacity to form HDL; (b) perturbation of genes in glucose and fatty acid homeostasis, influencing acetyl-CoA pools, promoting gluconeogenesis and glucose export; (c) elevated expression of ADIPOR2 suggesting increased sensitivity to adiponectin; (d) perturbations in genes of lipoprotein particle formation, differently for each statin; (e) perturbed expression of many metabolic genes that are directly controlled by nuclear receptors CAR and/or PXR. Conclusions: These data provide a novel global insight into hepatic effects of statins, offering biochemical explanations for higher blood glucose in statin-treated patients, and for drug-induced secondary fatty liver disease. Acknowledgements: This work was supported by the EU FP6 project STEROLTALK and by Slovenian Research Agency projects P1-0104 and J2-2197. Mateja Hafner was supported by the fellowship from the Slovenian Research Agency.