Fanconi anemia (FA) is a rare autosomal recessive disorder characterized by bone marrow (BM) failure and a wide array of physical abnormalities. Around 9% of FA patients develop acute myeloid leukemia (AML), which makes FA a good genetic model to study leukemogenesis. To date, however, no information exists on the functional integrity of the hematopoietic system of FA patients during the period in which they develop AML. Herein, we report on the characterization of hematopoietic progenitor cells from a pediatric FA patient that developed AML. Our results show that significant changes occurred in the hematopoietic system of the patient from the time he presented with FA to the time he developed AML. Such changes included marrow cellularity, frequency of CD34(+) cells and CFC, as well as proliferation potential of progenitor cells in liquid cultures supplemented with recombinant cytokines. Interestingly, no significant changes in the karyotype of marrow cells were observed, indicating that progression from FA into AML may proceed without major chromosomal alterations (i.e. translocations and/or deletions). This study represents one of the first steps towards the cellular characterization of the hematopoietic system in FA patients that develop AML.