AbstractObjectivesA QF‐PCR test has been developed to diagnose sex chromosome imbalances in prenatal samples and has been applied to a diagnostic service.MethodsThe test uses a PCR multiplex with eight primer pairs: six X‐chromosome polymorphic markers, including two markers from Xp (a region not included in previously published sex chromosome aneuploidy tests), one polymorphic marker for a locus common to the long arms of the X and Y chromosomes, and the non‐polymorphic amelogenin marker. Homozygosity for all X‐chromosome markers and the absence of the Y‐chromosome amelogenin marker is highly likely (907 : 1) to represent monosomy X (Turner syndrome), but interphase FISH is always used to confirm such a result.ResultsBlind studies were carried out to validate the test and the first year of clinical use has been reported. Results are usually issued within one working day, and the test is more efficient than interphase FISH.ConclusionsThe sex chromosome imbalance test has been targeted to prenatal samples displaying a clear ultrasound indication consistent with Turner syndrome, and has also been used to identify fetal sex in pregnancies at risk of inheriting a sex‐linked molecular disorder. No misdiagnoses were made. It is concluded that QF‐PCR can rapidly and accurately diagnose sex chromosome status and imbalances, reducing maternal anxiety and aiding in efficient pregnancy management. Copyright © 2003 John Wiley & Sons, Ltd.