In recent years, cytogenetics in combination with molecular methods has made rapid progress, resulting in new molecular cytogenetic methodologies such as fluorescence in situ hybridization (FISH). FISH is a molecular cytogenetic technique used for the detection of specific chromosomal rearrangements and applicable to many different specimen types. It uses fluorescently labeled DNA probes complementary to regions of individual chromosomes. These labeled DNA segments hybridize with the cytological targets in the sample and can be visualized by fluorescence microscopy in interphase nuclei or on metaphase chromosomes. Here, we describe the FISH methodology with centromeric probes for human cells, which is used in combination with the cytokinesis-block micronucleus assay and which allows discrimination between mutagens inducing DNA breakage (clastogens) or chromosome loss (aneugens).