Fanconi anemia (FA) is a congenital bone marrow failure syndrome in association with increased susceptibility to malignancy. We report the first in-depth description of a boy with FA who developed acute myeloid leukemia with complex hypodiploidy karyotype after successful stem cell transplantation. Of note, the leukemic cells consistently showed loss of heterozygosity (LOH) of the short arm of chromosome 17 (17p), which harbors the TP53 tumor suppressor gene. The complex hypodiploidy karyotype of the leukemic cells with LOH for 17p may represent a unique karyotypic profile that reflects genomic instability and thereby confers poor prognosis.