Introduction Oesophageal stricture is a frequent complication following repair of oesophageal atresia (EA). The aim of this study was to conduct a pre- and postintervention study and analyze the incidence of stricture formation and need for balloon dilatation after introducing prophylactic proton pump inhibitor (PPI) treatment.Children and Design All children operated for EA during 2001 to 2009 (n = 39) were treated with prophylactic PPIs (PPI group) for at least 3 months postoperatively. The frequency of stricture formation in the anastomosis and need for balloon dilatation was registered. A previously published group of children (n = 63) operated for EA during 1983 to 1995 not treated with prophylactic PPI was used as control group. Duration of follow-up time in the PPI group was equal to the one in the control group, and set to 1 year after the last oesophageal dilatation procedure.Results The PPI and control group were comparable regarding patient characteristics, gestational age and birth weight, prevalence of chromosomal aberration, and VACTERL (vertebral, and, cardiac, tracheal, esophageal, renal, limb) malformations. Also, survival rate and prevalence of surgery were similar in both groups. Mortality was mainly determined by associated malformations.The dilatation frequency needed in each child did not differ between the two groups. The prevalence of stricture formation was 42% in the control group compared with 56% in the PPI group, p = 0.25. Number of dilatations needed varied between 1 and 21, with a median value of 3 and 4, respectively, for the PPI and the control group. The children in the PPI group were significantly younger at the time of dilatation. This difference reflects a change in policy and increased experience.Conclusion The incidence of anastomotic stricture following repair for esophageal atresia remains high also after introduction of PPI. The results cannot support that prophylactic treatment with PPI prevent anastomotic stricture formation.