The choice of a probe is one of the most important considerations in fluorescent in situ hybridization technique. There are three types of FISH probes- whole chromosome painting probes, repetitive sequence/centromeric probes and locus-specific probes. Each type of probe has its own importance in the field of research, which is discussed in this review. Probes used for the diagnosis of different chromosomal abnormalities, genetically inherited diseases, gene mapping and localization of specific genes on chromosomes are reviewed. This helps the researchers in selection of probes based on their purpose of an experiment. This review also focuses on software tools for the construction of probes; companies providing readily available and customized probes according to the researcher's needs; laboratories offering their services in the field of molecular cytogenetics for the diagnosis of genetically inherited diseases, chromosomal anomalies and cancer. All data and materials collected in this review are related to references in this published article.