Chromosome microdissection is an extremely useful molecular cytogenetic tool for the characterization of chromosomal abnormalities in tumor cells. Although it has been used primarily in conjunction with fluorescence in situ hybridization (FISH), microdissection has also been useful for molecular analysis via microclone library construction. Recently, microdissection has been applied to the isolation of region specific cDNAs with sufficient success that gene discovery can now be added to the list of applications of this versatile molecular cytogenetic technique.