Williams syndrome (WS) is a rare genetic disorder caused by a microdeletion of chromosome 7q11.23. Although the mortality rate of patients with WS is not very high, sudden cardiac death can occur, particularly in cases complicated by coronary artery stenosis. A 3-month-old female infant with supravalvular aortic stenosis and peripheral pulmonary stenosis was discovered unconscious in bed by her mother. She was immediately transferred to an emergency hospital but succumbed despite multiple attempts as resuscitation. DNA microarray analysis revealed microdeletions of 7q11.23 and 16p11.2, confirming WS and unexpectedly identifying 16p11.2 deletion syndrome which is known to be associated with neurodevelopmental disorders. Postmortem computed tomography revealed a severely enlarged heart, indicative of cardiac dysfunction. External examination revealed moderate-to-severe developmental delays in height and body weight. The heart, on internal examination, revealed whitish-discolored lesions; histologically severe fibrotic changes and thickening of the intima in the coronary arteries and aorta. In the brain, the dentate gyrus of the hippocampus appeared malformed. Taken together, these findings suggest that the cause of death was cardiac dysfunction due to WS. In addition, it could be possible that 16p11.2 deletion syndrome and dentate gyrus malformation contributed to her death. Future autopsy studies are warranted to clarify the precise role of microdeletion disorders in sudden death to reduce future preventable deaths in children.