In a patient with nonketotic hypoglycemia, hyperammonemia, and a urinary organic acid pattern characteristic of glutaric acidemia type II, dysmorphic facial features and kidneys with multiple cortical cysts were the characteristic phenotypic findings. Electron microscopy revealed characteristic cytoplasmic, homogeneous, moderately electron-dense bodies with a limiting membrane. This specific lesion was noted in both central nervous system and renal tissues.