AbstractObjectiveThe objective of the study is to report the performance of noninvasive prenatal testing (NIPT) in twin pregnancies after the treatment of assisted reproductive technology (ART).MethodIn two years period, 565 pregnant women with ART twin pregnancies were prospectively tested by NIPT for screening for trisomy 21 (T21), 18 (T18), and 13 (T13) by sequencing cell‐free DNA in maternal plasma. Positive NIPT results were confirmed by karyotyping, while negative results were interviewed after delivery. Pregnant decision based on NIPT and confirmation results was discussed during post‐test counseling.ResultsIn total of 565 cases, NIPT had a failure rate of 0.9% (5/565). Four cases of T21 were identified by NIPT and confirmed by karyotyping, resulting in 100% (95%CI 39.8%–100%) positive predictive value. Among 556 cases with NIPT negative results, 506 cases (91.0%) were confirmed by follow‐up of postnatal phenotypes, while 33 cases (5.9%) had adverse pregnant outcomes with unconfirmed reasons because of the lack of cytogenetic samples. The remaining 17 cases (3.1%) refused follow‐up. No false negative result was reported.ConclusionWith apparently high positive predictive value and low false positive rate, NIPT has the potential to be used as a good alternative approach of conventional prenatal screening at the first trimester in ART twin pregnancy. © 2016 John Wiley & Sons, Ltd.