A case of clinically unsuspected fatal interrupted aortic arch (IAA) is described. A 17-day-old Japanese girl unexpectedly entered respiratory arrest at home. On autopsy, the heart was hypertrophic, with no apparent connection between the ascending and descending aortas. The ascending aorta branched into common carotid and right subclavian arteries, whereas the left subclavian artery arose from the descending aorta, which was supplied by the ductus arteriosus, indicating type B IAA. In addition, ventricular septal defect, bicuspid aortic valve, patent foramen ovale, and thymic aplasia were identified. The immediate cause of death was assumed to be "ductal shock." Because of the known strong association between type B and 22q11.2 deletion, her parents received genetic counseling and requested chromosomal analysis of the child. Fluorescence in situ hybridization worked well on a frozen blood sample, identifying the suspected deletion. This case was thus diagnosed as 22q11.2 deletion syndrome exhibiting IAA and thymic defect.