Purpose: In infants, the duodenum is the most frequently obstructed region of the gastrointestinal tract. The objective of the present study was to summarise the causes of early mortality and morbidity in infants with congenital duodenal obstruction (CDO). Methods: Data on a total of 94 patients with CDO diagnosed in our clinic, and treated surgically between January 1993 and December 2012, were studied retrospectively. Patients were divided into three groups in terms of diagnosis: annular pancreas (n = 45), duodenal atresia (n = 31), and duodenal web (n = 18). The groups were compared in terms of sex, birth weight, age at the time of operation, and morbidity and mortality rates. Results: Of the patients, 54 were males and 40 females, and the mean birth weight was 2,278 (range, 1,180-3,400) g. The average age at the time of the operation was 6.96 (range 1-38) days. The time to full oral intake postoperatively was 10.32 (range, 4-38) days. Additional anomalies were found in 61 (64.8%) cases. Early morbidity was most commonly associated with an anastomosis problem. Early mortality occurred in 6 (6.4%) cases, and the most common causes were sepsis and cardiac anomalies. Conclusions: Elimination of sepsis, cardiac anomalies, and anastomosis problems are critical to ensure continued reductions in infant mortality and morbidity caused by CDO.