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The aim of this double-blind, randomized, placebo-controlled study was to evaluate the effect of a prebiotic mixture on gastric motility in preterm newborns. After a feeding period of 15 days, gastric electrical activity was measured by electrogastrography, and the gastric emptying time was studied by ultrasound technique. No difference was seen in the daily increase of body weight, and no adverse events have been reported. The percentage of time in which propagation was detected in the electrogastrography signal was twice in newborns receiving formula with prebiotics with respect to placebo, and the gastric half-emptying time was 30% faster in the prebiotic group than the placebo group. Prebiotic oligosaccharides can modulate the electrical activity and the gastric emptying and may improve the intestinal tolerance of enteral feeding in preterm infants.