More than 5000 human diseases are caused by mutations within single genes. In many cases, the genomic location of the affected gene is known and this usually allows some form of molecular testing to determine whether a disease-causing mutation has been inherited by a pregnancy. Indeed, the gene may have been studied in such detail that mutations may be relatively easy to recognize. There is no doubt that molecular biology has transformed pre-natal diagnosis. However, there remain a number of congenital abnormalities, syndromes and metabolic disorders where patterns of inheritance suggest a single gene defect but where identification of the gene responsible, or its mutations, has so far proved elusive. In these cases, alternative forms of pre-natal diagnosis are still required.