Cigarette smoking is the major risk factor for developing chronic obstructive pulmonary disease, the fourth leading cause of deaths in the United States. Despite recent advances, the molecular mechanisms involved in the initiation and progression of this disease remain elusive. We used Affymetrix Gene Chip arrays to determine the temporal alterations in global gene expression during the progression of pulmonary emphysema in A/J mice. Chronic cigarette smoke (CS) exposure caused pulmonary emphysema in A/J mice, which was associated with pronounced bronchoalveolar inflammation, enhanced oxidative stress, and increased apoptosis of alveolar septal cells. Microarray analysis revealed the up-regulation of 1190, 715, 260, and 246 genes and the down-regulation of 1840, 730, 442, and 236 genes in the lungs of mice exposed to CS for 5 h, 8 days, 1.5 and 6 months, respectively. Most of the genes belong to the functional categories of Phase I genes, Nrf2-regulated antioxidant and Phase II genes, Phase III detoxification genes and others including immune/inflammatory response genes. Induction of the genes encoding multiple Phase I enzymes was markedly higher in the emphysematous lungs while reduced expression of various cytoprotective genes constituting ubiquitin-proteasome complex, cell survival pathways, solute carriers and transporters, transcription factors and Nrf2-regulated antioxidant and Phase II-responsive genes was noted. Our data indicate that the progression of CS-induced emphysema is associated with a steady decline in the expression of various genes involved in multiple pathways in the lungs of A/J mice. Many of the genes discovered in this study could rationally play an important role in the susceptibility to CS-induced emphysema.