Patients with Fanconi anemia (FA) tend to develop various hematologic and solid tumors. Cytogenetic abnormalities such as translocations of chromosome 1q, monosomy 5 and 7, trisomy 10, gains of 3q and t(8;21) have been reported in patients with FA who developed hematological malignancies. Since survival is low after the development of leukemia in FA patients, the follow-up for leukemia progression is very important. For this reason, cytogenetic anomalies that can be used as biomarkers in the development of leukemia are needed. Herein, we describe a patient with FA who developed acute myeloid leukemia with der(9)t(1;9) (q21;q34) for the first time.