To determine whether amnio-polymerase chain reaction (amnio-PCR) can replace conventional cytogenetic study for confirming the karyotype of fetuses in women with positive biochemical screening for fetal Down syndrome. To check the accuracy of this technique in our laboratory, we first compared the amnio-PCR results with those of conventional cytogenetic study in 235 patients referred from June 1999 to December 2001 for prenatal diagnosis in a referral center in Hong Kong. We then reviewed the results of 1526 amniotic fluid cultures performed for positive fetal Down syndrome screening between January 1997 and December 2001 and classified them as detectable or not detectable by amnio-PCR, using the assumption that we had replaced conventional cytogenetic study with amnio-PCR. The 235 amnio-PCR results were all informative, without a false-positive or false-negative result. Of the 1526 cases with positive fetal Down syndrome screening and no ultrasound abnormalities, only two cases of sex chromosome abnormalities and two cases of marker chromosomes would have been missed if conventional cytogenetic study had been replaced by amnio-PCR.Amnio-PCR can be an alternative to conventional cytogenetic study for women with positive biochemical screening for fetal Down syndrome and no demonstrable fetal structural abnormality.