This FISH application guide provides an overview of the principles and the basic techniques of fluorescence in situ hybridization (FISH) and primed in situ hybridization (PRINS), which are successfully used to study many aspects of genomic behavior and alterations. In 36 chapters, contributed by international experts in their particular field, the nowadays multiple approaches and applications of the powerful techniques are presented and detailed protocols are given. Described here are methods using various cell types and tissues as well as different organisms, such as mammalians, insects, plants and microorganisms. Multicolor FISH procedures and special applications such as the characterization of marker chromosomes, breakpoints, cryptic aberrations, nuclear architecture and epigenetic changes, as well as (array-based) comparative genomic hybridization studies are presented. Overall, the technique of choice is introduced for single cell analysis in human genetics, microbiology, animal and plant sciences.