Fluorescent in situ hybridization (FISH) as an adjunct technique to conventional banding techniques has been firmly established in the past few years. The many clinical and research applications of FISH include chromosome enumeration using alpha-satellite probes, marker identification, gene mapping and 'chromosome painting' in the delineation of complex structural chromosomal abnormalities. Comparative genomic hybridization (CGH) is a relatively new FISH-based technique which can detect gains and losses of whole chromosomes and subchromosomal regions. Like CGH, which can scan the whole genome without prior knowledge of specific chromosomal abnormalities, spectral karyotyping (SKY) confers on each chromosome a distinct colour to enable identification of even cryptic chromosomal rearrangements. The present paper introduces and summarizes these emerging molecular cytogenetic techniques.