We report on a patient with Fanconi's anemia (FA) who developed a myelodysplastic syndrome (RAEB-T) with complex karyotypic abnormalities (trp 1q23q42, monosomy 20, trisomy 13) at the age of 28. The patient achieved a complete hematological and cytogenetic remission after treatment with sequential high-dose cytosine arabinoside/mitoxantrone followed by G-CSF (5 micrograms/kg). Bone marrow hypoplasia was prolonged with 38 days of granulocytopenia < 500/microliters and 62 days of platelet transfusion dependency. Nonhematological toxicity did not exceed that of patients without underlying FA. Remission duration was 7 months. This observation shows the feasibility of high-dose Ara C treatment in patients with FA and MDS. Although hematopoiesis remained clonal in remission, the suppression of the cytogenetically abnormal clones transiently reversed the antecedent long-lasting pancytopenia.