Glycogen storage disease (GSD) and mucopolysaccharidosis (MPS) are both independently inherited disorders. GSD is a member of a group of genetic disorders involving enzymes responsible for the synthesis and degradation of glycogen. GSD leads to abnormal tissue concentrations of glycogen, primarily in the liver, muscle, or both. MPS is a member of a group of inherited lysosomal storage diseases, which result from a deficiency in specific enzymatic activities and the accumulation of partially degraded acid mucopolysaccharides. A case of a 16-month-old boy who presented with hepatomegaly is reported. The liver was four finger-breadth-palpable. A laboratory study showed slightly increased serum AST and ALT levels. The liver biopsy showed microscopic features compatible with GSD. The liver glycogen content was 9.3% which was increased in comparison with the reference limit, but the glucose-6-phosphatase activity was within the normal limit. These findings suggested GSD other than type I. Bony abnormalities on skeletal radiographs, including an anterior beak and hook-shaped vertebrae, were seen. The mucopolysaccharide concentration in the urine was increased and the plasma iduronate sulfatase activity was low, which fulfilled the diagnosis criteria for Hunter syndrome (MPS type II). To the best of the authors' knowledge, this is the first case of GSD and Hunter syndrome being identified at the same time.