Cytogenetic analysis is an important component of prenatal diagnosis. The ability to rapidly detect aneuploidy and identify small structural abnormalities of fetal chromosomes has been greatly enhanced by the use of molecular cytogenetic technologies. In this review, we will present some of the molecular cytogenetic techniques available to the clinical cytogenetics laboratory. These include fluorescence in situ hybridization (FISH), quantitative fluorescence PCR (QF-PCR), multiplex ligation-dependent probe amplification (MLPA) and microarray-based comparative genomic hybridization (array CGH). The benefits and limitations of each technology will be discussed in the context of prenatal diagnosis.