We report a case of moyamoya disease associated with Down syndrome and congenital heart malformations. Findings of cranial MR imaging indicated cortical laminar necrosis along with cerebral infarction. To explain the development of these findings, we hypothesized that hypoxic brain damage manifesting cortical laminar necrosis was caused by hypoperfusion of the brain due to occlusive changes to the cerebral vessels in moyamoya disease, in addition to a state of general hypoxemia secondary to congenital heart malformations.