OBJECTIVE Over the last 5 years, fluorescence in situ hybridization (FISH) techniques have had an important impact on molecular cytogenetic diagnosis, providing a better understanding of the role of numerical aberrations in hemopoietic neoplasms. The objective of this article is to analyze the clinical applications of FISH in the management of hemopoietic malignancies. METHODS The material examined in the present review includes articles and abstracts published in journals covered by the Science Citation Index and Medline, and personal published and unpublished data. BACKGROUND FISH technology has the advantage of being relatively simple, fast and flexible. Published data and ongoing prospective studies show that, under well-controlled experimental conditions, interphase FISH is more sensitive than conventional metaphase analysis in the detection of numerical abnormalities. Due to the relatively high rate of false positive results, FISH cannot be used for the study of minimal residual disease. However, since molecular strategies for the detection of small-sized aneuploid clones have not been developed yet, FISH represents a useful adjunct to conventional cytogenetics, especially for the quantitation of the size of abnormal clones during the course of the disease and to monitor XX/XY chimerism following sex mis-matched bone marrow transplantation. Different approaches to the study of multiple cell-lineage involvement by chromosome changes have been developed that take advantage of FISH techniques by: a) simultaneous FISH and membrane immunophenotyping of cytologic and histologic preparations; b) two-step analysis based on assessment of the morphology of cells on panoptical stains, with subsequent hybridization and relocation of previously identified cells; c) FISH analysis of enriched cell fractions obtained by cell sorting or by separation of bone marrow cells on a density gradient, and d) study of single hemopoietic colonies grown in semisolid media. CONCLUSIONS New molecular cytogenetic techniques, such as dual color FISH comparative genomic hybridization, are at hand that will greatly improve the diagnostic power of cytogenetics and make FISH increasingly useful in research laboratories as well as in clinical practice.