Respiration is controlled by the complex orchestration of central nervous system centers, peripheral chemoreceptors and muscles of respiration and is shaped by complex ontogenetic factors. Genetic defects can interfere with these factors, leading to the development of disorders of central control of breathing. Here, we briefly discuss the most important of these rare genetic syndromes: congenital central hypoventilation syndrome (CCHS), Rett’s syndrome (RTT), Prader-Willi syndrome (PWS) and Joubert syndrome. All these conditions are severe neurodevelopmental pathologies that can also involve other organs and systems and have specific genetic backgrounds that if correctly identified can enable better prognostic counseling of patients and/or caregivers. Treatment of disordered breathing is often necessary to counteract the life-threatening problems typical of CCHS and those that complicate the clinical course of RTT, PWS and Joubert syndrome.