Vitamin A (retinol) metabolites are ligands for transcription factors that regulate many genes. The liver is the main storage depot for retinol and plays a role in vitamin A homeostasis. To better understand the effects of vitamin A deficiency on liver gene expression, we produced retinol deficiency in male rats by feeding a diet low in retinol for 53 days after weaning and examined the effects on gene expression in liver using Affymetrix oligonucleotide microarrays. We detected expression of 41% of the 8799 probe sets represented on the RGU-34A GeneChips. Vitamin A deficiency resulted in major changes in liver gene expression: 805 genes (22% of all genes detected) differed at P<or=.05 (false discovery rate <0.143). Genes involved in fatty acid metabolism, peroxisomal function, glycolysis, glutamate metabolism and the urea cycle were altered. The expression of many sexually dimorphic genes was altered toward a feminized or senescent pattern of gene expression in the liver. Retinol deficiency also produces a shift toward increased protein and fat catabolism and decreased fatty acid synthesis.