We report on a case of acute myeloid leukemia in a 17-year old boy affected by Shwachman Diamond syndrome (SDS). Conventional cytogenetics at diagnosis revealed an abnormal clone with complex karyotypic changes including typical myeloid aberrations, such as monosomy 5, tetrasomy of chromosome 8, trisomy 9, and deletion of the short arm of chromosome 12. The boy was treated with conventional chemotherapy and reached complete remission of leukemia, confirmed by cytogenetics and fluorescence in situ hybridization. Nevertheless he failed to regenerate normal marrow cellularity and blood cell count. Cytogenetic information on hematologic malignancies in SDS patients are discussed.