The chapter considers specific treatment options, including allogeneic hematopoietic stem cell transplantation (allo-HSCT) in acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL), in patients with some prognostically proven cytogenetic variants as monosomal ones, complex and hyperdiploid karyotypes, like chromosomal translocations t(v;11)(v;q23), t(3;3)/inv(3); t(8;21), t(9;22), etc. Important prognostic role of additional chromosome abnormalities was shown for the patients with t(8;21) and t(9;22). Hence, it is evident that allo-HSCT in patients with poor risk cytogenetic variant must be performed as early as possible, i.e., during first complete remission.