We describe the first case of genetically diagnosed congenital dyserythropoietic anemia (CDA) type 1 in a Japanese man. The patient had hemolytic anemia since he was a child, and he developed diabetes, hypogonadism, and liver dysfunction in his thirties, presumably from systemic iron overload. When he was 48 years old a diagnosis was finally made by genetic analysis that revealed a homozygous mutation of CDAN1 gene (Pro1129Leu). His serum hepcidin-25 level was inappropriately low. We conclude that physicians should be aware of the possibility of CDA in a patient with anemia and systemic iron overload at any age.