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As the sensitivity and specificity of noninvasive prenatal testing (NIPT) that uses cell-free fetal DNA in maternal serum to identify Down syndrome (DS) in utero improves, NIPT could be considered a diagnostic test, thus avoiding the complications of chorionic villus sampling or amniocentesis. This study investigates the cost-effectiveness of NIPT as a diagnostic versus a screening tool.A decision-analytic model compared NIPT as a diagnostic tool (NIPT Dx) that did not require a confirmatory amniocentesis versus NIPT used for screening (NIPT Scr) that allowed a confirmatory amniocentesis for screen positive results. Baseline case, univariate, and multivariate sensitivity analyses were performed.For a high-risk population, NIPT Dx would result in three more DS babies born and 2432 more elective terminations compared with NIPT Scr. Furthermore, there would be many more terminations of fetuses without DS with NIPT Dx (2424) than procedure-related losses associated with NIPT Scr (29). NIPT Scr is more expensive but cost-effective at $7687 per quality-associated life year (QALY), less than the standard cost-effectiveness limit of $100 000/QALY.Noninvasive prenatal testing as a screening tool that requires a confirmatory amniocentesis is cost-effective compared with its use as a diagnostic tool and leads to far fewer losses of normal pregnancies. © 2013 John Wiley & Sons, Ltd.