Alveolar capillary dysplasia (ACD), which is a rare and lethal congenital pulmonary anomaly found in newborns, begins its onset or causes deterioration of the infant's condition some time after birth. Various congenital anomalies in combination with ACD have been reported, except for subglottic stenosis. Therefore, we aim to report a novel association in a case of ACD with the combination of atypical duodenal atresia and subglottic stenosis. The male infant was scheduled for duodeno-duodenostomy because a double-bubble sign was observed on a chest radiograph. He arrived at the operating theater without any symptoms. After induction of general anesthesia, although mask ventilation was performed without difficulties throughout the entire procedure, oxygen saturation values of the upper and lower extremities dissociated after several attempts of intubation. Surgery was canceled because of instability of the respiratory condition. Respiratory insufficiency worsened progressively, and the infant died at 5 days of age. An autopsy confirmed ACD and revealed cartilaginous subglottic stenosis, which had made intubation difficult. This report highlights the hazards of the onset and worsening of ACD, and the importance of thorough echocardiography before surgery when atypical duodenal atresia is suspected. Anesthesiologists should also be prepared for the difficulty of intubation.