Microscopic forms of karyotyping and cytogenetic analysis by means of G-banded chromosome analysis and rapid FISH (fluorescence in situ hybridization) on amniotic fluids or chorionic villus samples are at present regarded as the gold standard for prenatal diagnosis of chromosomal anomalies. Nevertheless, up to now the resolution of conventional chromosomal analysis was limited to approximately 4–5 Mb and not smaller than 2 Mb for FISH. Thus numerous common microdeletion syndromes are not detectable by conventional karyotyping. In addition, prenatal cells yield lower band resolution by conventional karyotyping than peripheral white blood cells making detection of subtle abnormalities even more difficult. With the advances in molecular-based techniques, a collaborative effort has led to the standardized method for detection of a restricted set of common chromosomal aneuploidies and microdeletion syndromes such as Down's syndrome, DiGeorge or Angelman syndrome either by rapid FISH and/or quantitative fluorescent PCR (QF-PCR). Even if the presence of particular phenotypic features of microdeletion or duplication syndromes may direct the use of syndrome-specific FISH tests in the postnatal period, syndrome-specific FISH analysis still has a very limited potential and application in the prenatal period due to the limitation in prenatal morphological or imaging diagnosis of many of the syndromes.