Despite the deleterious effects associated with elevated carbon dioxide (CO₂), or hypercapnia, it has been hypothesized that CO₂ can protect the lung from injury. However, the effects of chronic hypercapnia on the neonatal lung are unknown. Hence, we investigated the effect of chronic hypercapnia on neonatal mouse lung in order to identify genes that could potentially contribute to hypercapnia-mediated lung protection. Newborn mouse litters were exposed to 8% CO₂, 12% CO₂ or room air for 2 weeks. Lungs were excised and analyzed for morphometric alterations. The alveolar walls of CO₂-exposed mice appeared thinner than those of controls. Analyses of gene expression differences by microarrays revealed that genes from a variety of functional categories were differentially expressed following hypercapnia treatment including those encoding growth factors, chemokines, cytokines and endopeptidases. In particular and of major interest, the expression level of genes encoding surfactant proteins A and D (Sftpa1 and Sftpd) as well as Chloride channel calcium activated 3 (Clca3) were significantly increased, but the expression of WNT1 inducible signaling pathway protein 2 (Wisp2) was significantly decreased. The significant changes in gene expression occurred mostly at 8% CO₂ but only a few at 12% CO₂. Our results lead us to conclude that: 1) There are a number of gene families which may contribute to hypercapnia-mediated lung protection, and 2) the up-regulation of Sftp-A and Sftp-D may play a role as anti-inflammatory or antioxidant agents and 3) the effects of CO₂ seem to depend on the level to which the lung is exposed.