OBJECTIVE To determine age at diagnosis for congenital duodenal obstruction in the neonatal period and the relationship to clinical outcomes. METHODS A children's hospital database reflecting a 7 (1/2)-year period was reviewed to identify infants with the diagnosis of duodenal obstruction in the neonatal period. Infants were grouped according to time of diagnosis: antepartum, postpartum in-hospital or after hospital discharge. Clinical descriptors and outcome variables were assessed between infants in these three groups. RESULTS In total, 27/51 (53%) infants were diagnosed antenatally. Infants with prenatal diagnosis were less mature, more likely to have Down syndrome or other birth defects and the pregnancy was more likely to be complicated by polyhydramnios. Of the 24 infants diagnosed postnatally, 8 (33%) were diagnosed after hospital discharge. These infants tended to be breast fed and discharged before 48 h of age. They had greater weight loss and more metabolic disturbances at readmission for surgery. One infant in the late diagnosis group died. CONCLUSIONS Infants with congenital duodenal obstruction, particularly if breast fed, may not present with classical findings of upper gastrointestinal obstruction in the first days of life. Careful in-hospital evaluation of infants with persistent regurgitation, even low volume, is recommended to avoid missing this diagnosis.