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The effect of milk type on physiological, gastroesophageal reflux (GER) was studied in 37 breast-fed and 37 formula-fed, healthy, term neonates aged 2–8 days. The neonates were randomly selected from the public maternity ward and studied for 4 h after their morning milk feed. GER was recorded by a pH microelectrode placed 6 cm above the gastroesophageal junction and analyzed in the third and fourth postprandial hours. Sleep state was accurately defined from the electroencephalogram, electrooculogram, electromyogram, breathing, and behavioral observations. Movement was recorded from a piezo-electric transducer. In active sleep, the breast-fed neonates demonstrated GER episodes of significantly shorter duration than the formula-fed neonates. The means and 95% confidence intervals (CI) were 3.0 (1.6,5.2) compared with 8.3 (5.0,13.3) min/h of active sleep respectively (p < 0.05). This could not be explained by greater milk volume or increased movement before or during reflux in formula-fed neonates. However, the lower median pH values for GER in breast-fed neonates, 2.0 versus 2.5, were significantly different (p < 0.05). This difference may reflect more rapid gastric emptying. The lower esophageal pH is more likely to stimulate peristalsis and thus limit the duration of reflux (shorter episodes), in the breast-fed neonates.