ABSTRACTObjectiveEvaluate the results obtained from Quantitative Fluorescent (QF)‐PCR and conventional karyotype analysis to determine the advantages and disadvantages of dual testing in prenatal diagnosis.MethodsFrom 1 June 2006 to 1 June 2010, dual testing by QF‐PCR and karyotype analysis was performed in 13 500 prenatal samples. The rates of concordant results between the two methods were evaluated and the rates of clinically significant chromosomal abnormalities undetected by QF‐PCR were assessed.ResultsAbnormal karyotype was found in 320 out of 13 500 cases (2.37%, 95% confidence interval (CI) 2.11–2.63%). From these, QF‐PCR did not detect the abnormality in 70 cases (0.52%, 95% CI 0.4–0.64%), whereas 34 had a high/unknown risk of adverse outcome (0.25%, 95% CI 0.17–0.33%). By selectively applying dual testing only at cases with ultrasound findings and/or genetic history, 13 cases of high/unknown risk would have been missed (0.1%, 95% CI 0.05–0.15%).ConclusionSelective dual testing is expected to achieve a serious beneficial economical outcome and reduce parental anxiety produced by ambiguous cytogenetic findings. However, the percentage of 0.1% undetected clinically significant abnormalities cannot be ignored. A suggestion would include the offering of a choice to the pregnant women, undergoing prenatal screening, by informing them about different approaches and various complications. © 2012 John Wiley & Sons, Ltd.