The major causes of iron deficiency anemia (IDA) include iron loss due to bleeding, increased iron requirements, and decreased iron absorption by the intestine. The most common cause of IDA in Japanese women is iron loss during menstruation. Autoimmune atrophic gastritis and Helicobacter pylori infection can also cause IDA by reducing intestinal iron absorption. In addition to these common etiologies, germline mutations of TMPRSS6 can cause iron-refractory IDA (IRIDA). TMPRSS6 encodes matriptase-2, a membrane-bound serine protease primarily expressed in the liver. Functional loss of matriptase-2 due to homozygous mutations results in an increase in the expression of hepcidin, which is the key regulator of systemic iron homeostasis. The serum hepcidin increase in turn leads to a decrease in iron supply from the intestine and macrophages to erythropoietic cells. IRIDA is microcytic and hypochromic, but decreased serum ferritin is not observed as in IDA. IRIDA is refractory to oral iron supplementation, but does respond to intravenous iron supplementation to some extent. Because genetic testing is required for the diagnoses of IRIDA, a considerable number of cases may go undiagnosed and may thus be overlooked.