We report a case of Fanconi anemia in which cytogenetic analysis of bone marrow (BM) samples revealed two distinct karyotypes: 46,XY,dup(1)(q21q42), in the first sample and 46,XY,del(1)(q32) in the second, aspirated 7 months later after acute myeloid leukemia (AML) developed. We discuss the cytogenetic clonal fluctuation common in Fanconi anemia, with the Fanconi's anemia (FA) reports available in the literature. Interestingly, we have identified that del(1)(q32) has not been reported before in FA.