Fluorescence in situ hybridization (FISH) is rapidly becoming a commonly used technique in research as well as in the clinical setting. At present, FISH cannot replace traditional cytogenetics for routine prenatal diagnosis of chromosomal abnormalities. The technique has been improved over the fast few years with the use of directly labelled probes and multicoloured FISH allowing simultaneous detection of different sequence targets. The use of FISH provides cytogenetic information in a short time and by a relative simple technique. Performing FISH on interphase nuclei may provide preliminary results for cases with time constraints before formal cytogenetics results become available. Fluorescence in situ hybridization may also be used for rapid karyotyping in situations where metaphase nuclei cannot be made available such as retrieval of fetal cells in maternal blood or preimplantation genetic diagnosis on single blastomers obtained by in vitro fertilization. The Human Genome Initiative and the future unravelling of additional genetic loci will, no doubt, see an increasing use for this technique.