AbstractSudden unexplained deaths have been reported in 32% of Familial Dysautonomia (FD) subjects. To characterize cardiorespiratory dysregulation in children with FD that might contribute to potential sudden death, respiratory inductance plethysmography (chest/abdomen), ECG, hemoglobin saturation, and pulse waveform (VivoMetrics, Inc.) were recorded in the home during daytime wakefulness and overnight sleep in 25 children with IKBKAP mutation‐confirmed FD and 25 age‐, and gender‐matched controls. Breath‐to‐breath and beat‐to‐beat characterization of breathing, hemoglobin saturation, and heart rate was conducted. Children with FD had more frequent, prolonged, and severe episodes of hypoxemia than matched controls, awake and asleep. Though a small percent of the study time revealed bradycardia and apnea, the hypoxemia was the most prevalent pattern in FD and rarely occurred with related bradycardia. Though infrequent with desaturation or bradycardia, apnea was more prevalent in FD subjects than controls, and more apparent during sleep than wakefulness. Children with FD have cardiorespiratory dysregulation during wakefulness and sleep, likely representing alveolar hypoventilation. We hypothesize that the related repeated hypoxemia (and presumed related hypercarbia) may render individuals with FD more vulnerable to sudden death. Pediatr Pulmonol. 2008; 43:251–260. © 2008 Wiley‐Liss, Inc.