Several pathologies, such as central hypoventilation syndrome, central sleep apnea and cases of sudden infant death syndrome, involve defects in central breathing control. On a cellular and molecular level these disorders remain poorly defined and mechanistically not understood. A complex network of distinct brainstem neurons coordinates respiratory rhythm generation and modulation, which traditionally has been mapped by anatomical, physiological and pharmacological techniques. Recently, targeted gene inactivation of several transcription factors in mice was found to affect the development of specific groups of brainstem neurons and result in distinct respiratory phenotypes. These mutants promise a higher precision in the analysis of central breathing control and new diagnostic perspectives for respiratory syndromes, as indicated by the recent discovery of corresponding mutations in humans.