OBJECTIVE: To evaluate the effect of cisapride and chest physical therapy on the gastroesophageal reflux of wheezing babies. METHODS: We prospectively assessed the presence of technetium ((99)Tc) in the upper, middle, and lower esophagus of 25 wheezing babies (13 with GERD and 12 without GERD) using scintigraphy. Both groups underwent clinical investigation, including laboratory, X-ray and scintigraphy tests, for the etiology of the wheezing baby syndrome (WBS) and GERD. Expiratory Flow Acceleration (EFA) was performed before and after treatment with cisapride. The total time of GER episodes was accounted for each portion of the esophagus during scintigraphy and during EFA. RESULTS: Cisapride significantly reduced the total reflux time in the upper esophagus (P<0.05), but showed no influence during EFA. After cisapride therapy, EFA increased the total reflux time in the upper and medium esophagus; however, no statistical significance was found. Infants with GERD presented a shorter total reflux time in the distal esophagus (P<0.05) during EFA. After cisapride treatment, no statistical significance was found. Infants without GERD also presented reduced total reflux time in the distal esophagus during EFA (P<0.05). Those with GERD had increased total reflux time in the distal esophagus (P<0.05) before and after cisapride treatment during EFA and scintigraphy. CONCLUSIONS: Cisapride was effective in reducing the total reflux time, mainly in the upper esophagus. EFA apparently increased the number of episodes of GER, without achieving statistical significance. Further studies are necessary to investigate the effects of chest physical therapy according to body positions.