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To assess the prevalence of discrepant results found between quantitative fluorescent polymerase chain reaction (QF-PCR) analysis on uncultured prenatal samples and karyotyping on long-term culture.Results of QF-PCR from 1932 amniotic fluid (AF) and 1132 chorionic villus (CV) samples collected from September 1999 to February 2008 were analyzed. Nature of discrepancies was categorized for normal or abnormal results from uncultured and cultured samples.A total of nine (0.8%) discrepant cases were found in the CV and six (0.3%) in AF samples. Three abnormal results involving trisomy 18 or mosaic trisomy 13 showed normal karyotype with one representing complete discordance. There were three QF-PCR reports with initial mosaic trisomy 21 and five cases involving sex chromosome aneuploidy showing complete trisomy 21 and 45,X, respectively, after long-term culture.CV (0.8%) and AF (0.3%) samples showed discrepant results after culturing and 40% of discrepancy involved the sex chromosomes. QF-PCR on long-term culture was concordant with karyotyping results meaning that QF-PCR is technically sound. Discrepant PCR findings in uncultured prenatal samples likely arose from mosaicism or preferential cell culture. Limitations in abnormal QF-PCR results may be discussed with couples before further action.