The liver is a primary site for metabolism of xenobiotic compounds by enzymes which are dynamically regulated. Gene regulation in the liver also reflects the overall metabolic, energetic and hormonal state of the organism. Thus, we have generated a DNA Chip database to profile drug metabolism and toxic responses in rat liver. Rats were treated with four compounds which induce characteristic cytochrome P-450 genes. Gene expression was assayed in livers of these rats using Affymetrix DNA Chips. Induction of the expected cytochrome P-450 genes was observed, validating the approach. Additional regulatory responses were identified for genes encoding drug-conjugating enzymes and drug transporters for these well-studied compounds. Sex-specific expression of drug metabolic genes was also identified by comparing male and female rat livers. We encountered difficulties with DNA microarray technologies due to heterologous hybridisation between genes which share homology, or simple sequence repeats. We used cytochrome P-450 genes from four subfamilies to evaluate gene-to-gene hybridisation specificity using Affymetrix arrays. Gene-specific hybridisation was maximised by rational selection of DNA sequences to the array on the DNA chip.