The cytogenetic patterns in addition to the Philadelphia translocation in Philadelphia-positive (Ph+) ALL and chronic myeloid leukemia (CML) is heterogenous. We investigated 154 patients with Ph+ ALL at diagnosis or at relapse and 174 patients with different phases of CML. Ph+ ALL at diagnosis demonstrated a heterogenous pattern with a high frequency of numerical and structural chromosomal aberrations. CML at diagnosis presented with rare additional chromosomal changes. In Ph+ ALL, the pathway from diagnosis to relapse was characterized by the acquisition of a higher number of chromosomal aberrations, but the pattern of frequent aberrations at relapse did not differ from that observed at diagnosis. In contrast, in CML the pathway from chronic to the advanced phases was characterized by the acquisition of new chromosomal changes and by the development of karyotype complexity. In addition, the investigation of 10 cases of lymphoid blast crisis of CML showed significant differences in the karyotype in comparison to Ph+ ALL at diagnosis. Therefore, the karyotype can be helpful in discriminate de novo lymphoid blast crisis of CML from de novo Ph+ ALL. In conclusion, we were able to demonstrate that the cytogenetic patterns of Ph+ ALL and of CML are different at diagnosis and furthermore follow different pathways during progression or relapse.