BACKGROUND: The use of thickeners is a standard therapy for decreasing episodes of regurgitation or vomiting in infants. However, it remains to be investigated whether thickener is effective for vomiting and/or chronic respiratory symptoms in children with cerebral palsy. METHODS: We enrolled 18 neurologically impaired children caused by cerebral palsy, with gastroesophageal reflux disease. In the first part of this study (pH monitoring), subjects were randomly allocated to two groups: fed with a high-pectin diet [enteral formula: pectin liquid = 2:1 (v/v)], or a low-pectin diet [enteral formula: pectin liquid = 3:1 (v/v)]. Two-channel esophageal pH monitoring was performed over 48 h. In the second part (clinical trial), subjects were fed a high- or low-pectin diet and non-pectin diet for 4 weeks in a crossover manner. Nurses recorded the feeding volume, number of episodes of vomiting, volume of gastric residue, episodes of cough and wheeze, frequency of using oxygen for dyspnea, and the day when the child could return to school. Cough and wheeze were recorded as a cough-score. RESULTS: The median value for the % time pH < 4 at the lower and upper esophagus was significantly decreased with a high-pectin diet [9.2% (6.2-22.6) vs. 5.0% (3.1-13.1); P < 0.01, 3.8% (2.9-11.2) vs. 1.6% (0.9-8.9); P < 0.01 (interquartile range), non-pectin and high-pectin, respectively]. The number of reflux episodes per day and duration of longest reflux were decreased significantly with a high-pectin, but not with a low-pectin diet. The median number of episodes of vomiting decreased significantly with a high-pectin diet [2.5/week (1.0-5.0) vs. 1.0 (1.0-1.5), P < 0.05]. The median cough-score was significantly decreased by both concentrations of pectin [8.5/week (1.0-11.5) vs. 2.0/week (0.0-3.0), fed with a high-pectin diet; 7.0/week (1.0-14.5) vs. 1.0/w (0.0-5.0), fed with a low-pectin diet, P < 0.05]. CONCLUSION: Pectin liquid partially decreased gastroesophageal reflux as measured by eshophageal pH monitoring, and might improve vomiting and respiratory symptoms in children with cerebral palsy. TRIAL REGISTRATION: ISRCTN19787793.