Molecular techniques have been developed for prenatal diagnosis of the most common chromosome disorders (trisomies 21, 13, 18 and sex chromosome aneuploidies) where results are available within a day or two. This involves fluorescence in situ hybridization (FISH) and microscopy analysis of fetal cells or quantitative fluorescence polymerase chain reaction (QF-PCR) on fetal DNA. Guidance is provided on the technological pitfalls in setting up and running these methods. Both methods are reliable, and the risk for misdiagnosis is low, although slightly higher for FISH. FISH is also more labour intensive than QF-PCR, the latter lending itself more easily to automation. These tests have been used as a preamble to full chromosome analysis by microscopy. However, there is a trend to apply the tests as 'stand-alone' tests for women who are at relatively low risk of having a baby with a chromosome disorder, in particular that associated with advanced age or results of maternal serum screening programmes. These women comprise the majority of those currently offered prenatal diagnosis with respect to fetal chromosome disorders and if introduced on a larger scale, the use of FISH and QF-PCR would lead to substantial economical savings. The implication, on the other hand, is that around one in 500 to one in 1000 cases with a mentally and/or physically disabling chromosome disorder would remain undiagnosed.