Oxygen desaturation during sleep in patients with cystic fibrosis has been attributed to changes in the end-expiratory volume during rapid eye movement (REM) sleep, leading to worsening of the ventilation-perfusion distribution. The purpose of this study was to describe the changes in ventilation during sleep that may contribute to the oxygen desaturation. Six adolescent males with moderate to severe cystic fibrosis were studied. It was concluded that hypoventilation during REM may contribute to oxygen desaturation in patients with cystic fibrosis.