Cytogenetic abnormalities occurs in almost half of myelodysplastic syndrome (MDS) patients and are considered to be the most important prognostic factor for survival, so they have been included in the International Prognostic Scoring System (IPSS) since 2007. Complex karyotype (CK) is defined as more than or equal to 3 independent chromosomal abnormalities at the same metaphase and is an independent poor prognostic factor, usually associated with a shorter median overall survival and propensity toward malignant transformation. From January 2008 through June 2022, 1744 patients with suspected or diagnosed hematological neoplasms (including MDS/AML) who had a bone marrow evaluation and concurrent conventional karyotype were identified. Karyotyping was successfully performed on 1167 (67%) of 1744 patients. In total, 914 (54%) with an adequate karyotypic analysis carried out a diagnosis of myelodysplastic syndrome. Among the cases, 9,7% were classified as complex karyotype. Del(5q)/-5 was identified in 52% of patients with complex karyotype, followed by chromosome 11 and chromosome 7 as well as chromosome 17 abnormalities, accounting for 38%, 23% and 23%, respectively. Besides, complex karyotype patients with translocations and derivation involvements, accounted for 28% and 14%, respectively. It is likely that pathogenetic mechanisms in del(5q) may involve hemizygous mutations or haploinsufficiency and be modified by additional somatic lesions affecting genes on other chromosomes. This report shows that the presence of deletion 5q may be the first step to the development of complex karyotype and is a determinant key of the genetic and genomic complexity and clonal hierarchy in MDS with 5q abnormalities.