Complex karyotypes (CK) were thoroughly analyzed by using the data of multicolor FISH in 27 patients with myelo-dysplastic syndromes (MDS) and MDS-associated acute myeloid leukemias (AMLm). Despite a vast variety of identified genetic impairments, chromosomes 5, 8, and 7 appeared to be most frequently (79 %, 76 %, and 73 %, respectively) involved in rearrangements, a fact also documented in literature. In view of this, two independent cytogenetic subgroups with chromosome 5/7 and 5/7/8 rearrangements were formed. Chromosomes 5 and 7 predominantly showed unbalanced karyotype, and chromosome 8 was characterized by its combinations with trisomies. The study also revealed that complex markers, more often than the other ones, contain chromosome 7 material, which has not so far been adequately explained. At the same time, the accumulation of chromosome 8 material in CK was associated with a more favorable course of underlying disease. On the other hand, detailed structural analysis of some supercomplex CK markers affords grounds for the assertion that chromothripsis notably participates in their formation. The overall survival of MDS and AMLm patients in artificially formed joint subgroups with combinations of involved chromosomes 5/7 and 5/7/8 was significantly lower than in AMLm (p = 0.035).