We evaluated the outcome in infants with esophageal atresia (EA) treated in our department over the last two decades. The medical records of 147 infants treated from 1986 to 2005 were reviewed. Patient characteristics, associated anomalies, surgery and complications were recorded. We divided the material into two time-periods: 1986-1995 and 1996-2005; 125 patients or parents were interviewed regarding gastrointestinal function, respiratory symptoms and education. The incidence of major cardiac defects increased from 23 to 29% and the overall survival increased from 87 to 94%. Using Spitz' classification survival increased from 93.5 to 100% in group I and from 68.4 to 77.8% in group II. In group III, during the second time period, survival was 100% in three patients. The incidence of anastomotic leakage and recurrent fistula did not change over time. The rate of anastomotic strictures increased from 53 to 59% between the two time-periods. A primary anastomosis could be done in 85% of the patients during the second period versus 78% of the patients during the first period. Anti-reflux surgery was done in only 11 and 9%, respectively, during the two time-periods. In patients who were 16-20 years old, 40-50% had gastrointestinal and respiratory symptoms. Ninety percent of the patients attended normal school. The major difference between the periods 1986-1995 and 1996-2005 was an increased survival despite an increased incidence of major cardiac defects. Gastrointestinal and respiratory symptoms were frequent. Long-term follow-up and treatment of complications of esophageal atresia is important for this patient group.