Hyperimmunoglobulin D and periodic fever syndrome (HIDS) is an autosomal recessive auto-inflammatory disorder characterized by recurrent febrile attacks with lymphadenopathy, abdominal distress, skin eruptions and joint involvement. We discuss the case of a 15-year-old Japanese girl who had presented with periodic fever, hepatosplenomegaly and intractable diarrhea from seven weeks of age. At first, undifferentiated autoimmune disorder was suspected, and she was treated with prednisolone and, in turn, with immunosuppressants such as cyclosporine, methotrexate, cyclophosphamide and rituximab or with plasma exchange. However, these trials failed to relieve her symptoms, and so she was transferred to our hospital when she was 15 years old. Her parents and elder brother had no history of recurrent fever, prolonged abdominal pain or diarrhea of unknown origin. The patient had extremely elevated levels of mevalonic aciduria and had homozygosity as a novel mutation in the MVK gene (G326R). Finally, HIDS was diagnosed. She was treated with simvastatin, which resulted in a moderate decrease of the urinary mevalonic acid concentration and good clinical course. This is the first case in which homozygosity for the mutation of the MVK gene has been reported in an Asian patient, and indicated a need for differentiation.