Fluorescence in situ hybridization, or FISH, was developed in the early 1980s and has quickly become one of the most widely used techniques in cytogenetics. Labeled probes are used to bind complementary DNA or RNA sequences on a chromosome or in a region within a cell. Earlier, the probes could only be obtained by cloning or reverse transcription of a DNA template. Currently, the probe oligonucleotides can be synthesized synthetically. Additionally, with the advancement of optical techniques, CCD cameras, and sophisticated image-processing software, FISH signals can be interpreted with greater sensitivity and high specificity.

These technological advances have widened the scope of FISH applications from cytogenetics and gene mapping to the diagnosis of genetic and infectious diseases. High-resolution images obtained from FISH help identify chromosomal aberrations, such as common aneuploidy (abnormal number of chromosomes in a cell), microdeletion/microduplication syndromes (loss or gain of a chromosome), and subtelomeric rearrangements.

FISH is also used to detect the presence of microbial pathogens in human blood cells. In such diagnostic assays, short fluorescence-labeled DNA binds to the microbial 16s rRNA and can be visualized under a fluorescence microscope. It helps in the identification of the infectious agents at the genus or species level. FISH-based diagnostics allows for rapid identification of the pathogen, which is crucial for detecting slow-growing organisms like Mycobacteria - causative agent of tuberculosis or other microbes, such as Tropheryma whipplei that are difficult to culture.