Molecular cytogenetics is a new branch of chromosome research that is just is just over 25 years old. Current applications of fluorescence in situ hybridization (FISH) in diagnostics and research are summarized in this chapter. An overview of both DNA- and RNA-based in situ hybridization is provided. The application of molecular cytogenetics to inherited and acquired diseases is reviewed, including pre- and postnatal, preimplantation and tumorcytogenetic diagnostics. The use of FISH in gene mapping, mutagenesis, microbiology, interphase cytogenetics and ZOO-FISH is also reviewed, and the overall strengths and limitations of FISH in all of these fields are discussed.