Dietary phytosterols significantly reduce plasma cholesterol concentrations and atherosclerosis in apolipoprotein E-knockout (apo E-KO) mice. We investigated the long-term effects of phytosterol treatment on gene expression in the liver of these mice. Male apo E-KO mice were fed an atherogenic diet supplemented with (n=6) or without (n=6) 2% (wt/wt) phytosterol mixtures for 14 weeks. Liver specimens were collected and stored in RNAlater immediately. mRNA was extracted and subjected to microarray analyses and real-time quantitative reverse transcription-polymerase chain reaction (RT-PCR) assay for confirmation. Oligonuleotide microarray analysis of pooled samples (n=3) revealed that the expression of 132 genes/transcripts was significantly altered in treated animals, considering the false discovery rate (FDR) of 0.23. Real-time RT-PCR techniques confirmed these alterations in the expression of several of these genes, including Hmgcr (2.16-fold; P=.0002), Hmgcs1 (1.79-fold; P=.001), Hsd17b7 (2.11-fold; P=.028), Sqle (2.03-fold; P=.01), Cyp51 (1.8-fold; P=.001), Fads1 (1.55-fold; P=.031), Fads2 (2.17-fold; P=.047), Lpin1 (3.67-fold; P=.001), Ppargc1b (PGC-1beta; a coactivator of sterol-regulatory element-binding proteins; 1.66-fold; P=.007) and Cyp7B1 (1.81-fold; P=.025). In summary, our data suggest that long-term dietary phytosterols can alter the expression of a number of hepatic genes that regulate sterol metabolism in apo E-KO mice. It is possible that these changes are due to inhibition of cholesterol absorption, but are not a direct effect of plant sterols. Further multivariate correlation or association analysis is needed to establish the relations between changes in the expression of these genes and prevention of atherosclerosis by phytosterols.