Advances in the treatment of aplastic anemia (AA) have led to the long-term survival of nontransplanted AA patients; however, the issue of subsequent hematological clonal disorders has been raised as some AA patients treated with immunosuppressive therapy or granulocyte-colony stimulating factor (G-CSF) went on to develop myelodysplastic syndromes (MDS) and/or acute myeloid leukemia (AML) with the frequent presentation of monosomy 7. We report a case of AA progressing to overt MDS/AML following 11 years of treatment that included immunosuppressive therapy and G-CSF. The patient's MDS/AML proved refractory to therapy including myeloablative treatment with allogenic peripheral blood stem cell transplantation. Earlier reports and the present case strongly suggest that there is no recurrent chromosomal aberration other than monosomy 7 in cases of AA that progress to MDS/AML. To our knowledge, ours is the first reported case of a t(3;5)(p25;q31) among AA patients that have progressed to MDS/AML.