In the last decade a variety of fluorescence in situ hybridization (FISH) assays have been developed. In this paper we present an overview on the currently available methods in molecular cytogenetics, highlighting their advantages and limitations, as well as their applications. Even though one has to be impressed by the total number of new techniques introduced in molecular cytogenetics, one has to be aware of the fact that it is not the brilliance of a technique that is important but the scientific question that can be addressed by it. In this review special emphasis has given in describing possible strategies for the characterization of marker and derivative chromosomes in tumor- and clinical cytogenetics.