Fescue toxicosis affects wild and domestic animals grazing fescue pasture infected with the endophytic fungus Neotyphodium coenophialum. Signs of fescue toxicosis include increased core body temperature and respiration rate and decreased milk yield and reproductive performance. Laboratory mice also exhibit symptoms of fescue toxicosis, as indicated by reduced growth rate and reproductive performance. Mice were used to study the effects of fescue toxicosis on hepatic gene expression. Twenty-seven mice were randomly allocated to a diet containing either 50% endophyte-infected (E+; 6 ppm ergovaline) or endophyte-free (E-) fescue seed for 2 wk under thermoneutral conditions. Liver genes differentially expressed due to fescue toxicosis were identified using DNA microarray. A 2-stage ANOVA of microarray data identified 36 differentially expressed genes between mice fed E+ and E- diets. Another analysis method, significance analysis of microarray, identified 9 genes as differentially expressed between treatment groups, and some genes overlapped with genes identified by ANOVA. Hierarchical clustering of 36 genes identified by ANOVA clearly separated the mice by diet, with 100% confidence as computed by bootstrap analysis. Expression of 11 genes was verified using quantitative real-time PCR. The E+ diet resulted in downregulation of genes involved in the sex-steroid metabolism pathway and genes involved in cholesterol and lipid metabolism. Genes coding for ribosomes and protein synthesis were upregulated by the E+ diet. Genes identified in the present analysis indicate some of the mechanisms by which fescue toxicosis occurs in animals.