We carried out chromosomal analysis of a 33-year-old male who was diagnosed as having aplastic anemia. The patient showed severe pancytopenia, a normal NAP score, hypoplastic marrow and no myelodysplastic changes. 45,XO was found in all bone marrow cells examined, and in 10% of peripheral blood cells examined. To our knowledge, this is the first reported case of male aplastic anemia to show loss of the Y chromosome in all bone marrow cells examined, and this case may suggest a possible mechanism of juvenile onset of aplastic anemia.