Fiberoptic bronchoscopy was performed in 15 normal nonsmokers and in 15 smokers without cancer. The right upper lobe carina was brushed, and RNA was extracted and processed (U133A Genechip; Affymetrix; Santa Clara, CA) [approximately 22,500 genes]. Filter criteria for the quality of a sample were developed, and data were analyzed using a variety of computational algorithms. In nonsmokers, the variation in the expression level of genes among subjects was small. Multiple linear regression revealed that age, sex, and race had little effect on the nonsmoker transcriptome, as < 2% of the gene expression levels were associated with any of these three variables at the p < 0.01 level. Using a t test, 206 genes (4%) differed between smokers and nonsmokers at p < 0.01, and 610 genes differed at p < 0.05. The greatest increases in smokers occurred in genes associated with cell adhesion, detoxification, and secretion. The greatest decreases were in immune-regulatory genes and cytokeratins, with the decrease in the latter suggesting a change in epithelial cell differentiation. Linear regression analysis showed that the expression of 95 genes correlated (p < 0.01, R ≥ 0.6) with the number of pack-years of smoking in smokers.