In situ Hybridization (ISH) is a powerful technique for precise detection and localization of a specific nucleic acid sequence within a histologic section. The underlying principle of ISH is that the nucleic acids within a histologic specimen can be detected by the hybridization of a complementary nucleic acid probe in which a reporter molecule is attached. Common non-radioactive labels for probe are fluorescein and digoxigenin. Subsequent visualization of the reporter molecule localizes DNA or RNA sequences in tissue or cells samples.

There are two basic approaches to visualize the DNA or RNA target sequences in situ: chromogenic in situ hybridization (CISH) and fluorescence in situ hybridization (FISH). While these approaches involve the same underlying principle, the instrumentation required to visualize the specimen is different.

ISH has broad applications such as chromosome mapping, karyotyping, and pathogen profiling. Nucleic acid probe also enables the localization and analysis of gene expression profile as well as other types of RNA such as microRNA and long non-coding RNA.