ABSTRACT Objective This study aimed to provide an individualized assessment of fetal trisomy 21 and trisomy 18 status for twin pregnancies by maternal plasma DNA sequencing. Method Massively parallel sequencing was performed on the plasma/serum DNA libraries of eight twin pregnancies and 11 singleton pregnancies. The apparent fractional fetal DNA concentrations between genomic regions were assessed to determine the zygosities of the twin pregnancies and to calculate the fetal DNA concentrations of each individual member of dizygotic twin pairs. Z‐scores were determined for the detection of trisomy 18 and trisomy 21. Results Circulating DNA sequencing showed elevated chromosome 21 representation in one set of twins and elevated chromosome 18 representation in another pair of twins. Apparent fractional fetal DNA concentration analysis revealed both sets of twins to be dizygotic. The fractional fetal DNA concentrations for each individual fetus of the dizygotic twin pregnancies were determined. Incorporating the information about the fetal DNA fraction, we ascertained that each fetus contributed adequate amounts of DNA into the maternal circulation for the aneuploidy test result to be interpreted with confidence. Conclusion Noninvasive prenatal assessment of fetal chromosomal aneuploidy for twin pregnancies can be achieved with the use of massively parallel sequencing of cell‐free DNA in maternal blood. © 2013 John Wiley & Sons, Ltd. What's already known about this topic? By using massively parallel maternal plasma DNA sequencing, noninvasive prenatal detection of fetal chromosomal aneuploidies has been achieved. The sensitivity of the maternal plasma DNA sequencing test for aneuploidy detection is governed by the fractional fetal DNA concentration. What does this study add? We have recently developed a maternal plasma DNA sequencing‐based method for the noninvasive assessment of twin zygosity. The method also allows the determination of the fetal DNA fraction contributed by each member of a pair of dizygotic twin in maternal plasma. In this study, we applied the new method to two dizygotic twin pregnancies involving one aneuploid fetus each. We confirmed that each fetus contributed adequate amounts of DNA into maternal plasma so that the aneuploidy test result could be interpreted with confidence.