Hematological malignancies comprise a group of neoplasms that arise through malignant transformation of bone marrow derived cells. The diagnosis of the hematologic malignancies presents a challenge due to the complexity of hematopoiesis that gives rise to a number of biologically and clinically distinct neoplasms. In the last decades, molecular markers supplied by immunophenotyping and cytogenetic/molecular genetic analysis have become of crucial importance for understanding pathogenesis, making a precise diagnosis, determining prognosis, choosing treatment and developing new forms of treatment. Advances in molecular genetic research enabled a better understanding of the mechanisms by which chromosomal events cause blood malignancies. New molecular discoveries are also helpful to direct research toward novel targeted therapies.