The nasal epithelium is an important target site for chemically induced toxicity and carcinogenicity. Gene expression data are being used increasingly in studies of such conditions. In order to provide normal baseline data for this target organ, we investigated gene expression profiles in nasal transitional and respiratory epithelium of healthy rats. We collected cells lining the anterior nasal passages, as confirmed by light microscopy, into 200 μl of Trizol reagent by controlled intranasal instillation. We performed gene expression analysis using Clontech complementary DNA Rat Atlas 1.2 arrays (approximately 1,200 genes) and verified selected transcripts using the polymerase chain reaction with reverse transcription (Taqman). The percentages of genes within specific average expression ranges, on the basis of phosphorimager signal intensities, were 1.4% at 3,000–45,000, 3.3% at 1,000–3,000, 30.1% at 100–1,000, and 65.2% below 100. The most highly expressed genes included those involved in phase I (for example, cytochrome Ps) and phase II (for example, glutathione S-transferases) xenobiotic metabolism, bioenergetics (for example, cytochrome oxidase), osmotic balance (for example (Na++K+)ATPase) and epithelial ionic homeostasis (for example, ion channels). These findings are consistent with normal nasal epithelial functions. Such baseline data will contribute to a further understanding of the functions of this region of the respiratory tract and facilitate the interpretation of treatment- or disease-related responses by the nasal epithelial transcriptome.