Primary and secondary chromosomal abnormalities play an important role in the characterization of biological, pathological, and clinical subgroups of malignant lymphomas. The introduction of fluorescence in situ hybridization (FISH) and the combination of immunophenotyping plus FISH to the diagnosis of lymphatic neoplasms allows the fast and sensitive detection of specific chromosomal changes and provides new insights into the genetic basis of lymphomagenesis. This article reviews the possibilities and limitations of molecular cytogenetic techniques in comparison to cytogenetic and molecular genetic methods and discusses their clinicopathological impact for non-Hodgkin's lymphoma and Hodgkin's disease.