A 14-year-old boy was referred to our hospital with general fatigue and sore throat. A chest X-ray and computed tomography revealed diffuse bilateral bronchitis. A laboratory examination showed anemia, thrombocytopenia, and renal insufficiency. He had a past medical history of hemolytic uremic syndrome (HUS) without diarrhea at the age of 3; moreover, his elder brother suffered from HUS at the age of 12. These findings indicated that the patient had a familial relapsing form of HUS (atypical HUS). Therefore, he was immediately treated with plasma exchange (PE), as suggested by guidelines, obtaining complete remission. Fifteen months later, he suffered another relapse of atypical HUS preceded by respiratory infection and was cured again with PE. His ADAMTS-13 activity was normal and its inhibitory antibody was undetectable. Two different mutations were found in the gene encoding membrane cofactor protein (MCP). Respiratory infections preceded all three episodes of HUS, but we could not detect the pathogenic agent. Although the longterm outcomes of patients with atypical HUS who have mutations in the MCP gene appear favorable, recurrences are nevertheless frequent. Few reports have described Japanese patients with atypical HUS and complement regulatory abnormalities. This is the first report of a Japanese patient with atypical HUS and mutations in the MCP gene.