We studied the prognostic significance of combination of different chromosomal abnormalities and genomic mutations in Ph+ chronic myeloid leukemia patients. In general 49 cytogenetic analyses of bone marrow aspirate from 35 patients (11 of these observed in dynamics) have been carried out. The additional chromosome changes were found in 25.07% cases and approximately 80% of anomalies appeared in the blast phase. Among the secondary chromosomal abnormalities extra Ph-chromosome appeared mostly in different combinations with trisomy of chromosomes 8 and 19. Appearance of clonal differences of cells, high rate of genome mutations and of microchromosomes had negative prognostic significance on disease proceeding.