We studied the effects of positional treatment and cisapride (a new prokinetic agent) on the incidence and duration of gastroesophageal reflux in 22 infants (4–26 weeks old) in asleep, awake, fasted, and postcibal periods. In addition to gastroesophageal reflux (assessed by 24-h continuous esophageal pH monitoring), all infants presented with a disrupted irregular sleep pattern (“respiratory dysfunction”) (assessed by a simultaneously performed cardiopneumogram). Reflux was particularly prominent during the sleep and fasted periods. Investigations (cardiopneumogram and esophageal pH monitoring) in the study population were repeated under treatment conditions (cisapride) after 13–16 days. All pH monitoring data with regard to the total investigation time decreased significantly (p < 0.001). The treatment-related differences were largest in the asleep and fasted periods, but treatment data were not completely within normal ranges (established in age-matched asymptomatic infants), as they were for the awake periods. Associated symptoms of gastroesophageal reflux (belching, cough, nocturnal wheezing, irritability, and restlessness at night) were evaluated before and during treatment by history. A combination of positional treatment and cisapride seemed effective (objectivated by pH monitoring data and clinical improvement); cisapride did not cause adverse reactions. The disrupted sleep pattern improved significantly or disappeared (p < 0.001) in all infants. These data suggest that in a number of young infants, gastroesophageal reflux may be associated with a disturbed, irregular sleep of poor quality, which is characterized by a typical breathing pattern (multiple, irregularly repeated, short apneas).