Adaptation to air breathing at birth is dependent on formation and function of the lung. Lung morphogenesis is a complex process dependent on precise temporal-spatial control of cell proliferation, differentiation and behavior mediated by autocrine-paracrine signaling that instructs transcriptional processes during organogenesis. Mutations in genes causing severe, and often lethal, lung malformations include those in the sonic hedgehog, fibroblast growth factor and thyroid transcription factor-1 pathways. Mutations in genes regulating surfactant homeostasis, necessary for reduction of surface tension in the alveoli, cause lethal respiratory distress at birth or interstitial lung disease in childhood. Inherited disorders of the surfactant system that affect neonatal respiratory adaptation at birth include hereditary surfactant protein B deficiency, mutations in surfactant protein C and the ABCA3 transporter.