The pulmonary surfactant has a complex metabolic cycle that includes synthesis with post-translational processing, secretion, clearance, reuptake, and recycling. The authors and others have shown that mutations in SFTPB, SFTPC, and ABCA3 disrupt different steps in this cycle, alter surfactant function, and cause respiratory distress with diverse clinical presentations in newborn infants, older children, and adults. Currently available genetic diagnostic methods permit rapid evaluation of common pathologic mutations. Lung biopsy may be necessary if initial genetic diagnosis is inconclusive. As other genes involved in the surfactant metabolic cycle are characterized, genetic evaluation for defects in surfactant synthesis will expand. New, high throughput genomic technologies will permit rapid screening of multiple genomic sites in large numbers of genes and will suggest novel therapeutic targets to improve outcomes for affected infants and children.