A full-term newborn infant is described with recurrent episodes of oxygen desaturation and apnea on the day of birth. The apnea did not improve with continuous positive airway pressure (CPAP) and intermittent nasal ventilation, therefore intubation and mechanical ventilation were required. A preliminary diagnosis of congenital central hypoventilation syndrome (CCHS) was made with the use of simultaneous measurements of end-tidal CO2 (EtCO2) and a diaphragm electrical activity waveform that was detected using microsensors placed on the infant's feeding tube. It was observed that during deep sleep, the diaphragm electrical activity waveform was close to 0 μV (central apnea) and EtCO2 levels rose accordingly (central hypoventilation). Genetic testing subsequently revealed a Phox2b mutation, establishing the diagnosis of CCHS. Simultaneously measuring diaphragm electrical activity and EtCO2 is feasible and may be a valuable bedside diagnostic tool in cases of suspected CCHS before the diagnosis is confirmed with genetic testing.