Objectives To explore the accuracy of sex chromosome aneuploidy detection when clinically applied MPS-based noninvasive fetal aneuploidy test in Southwest hospital and investigate the accuracy of this method in noninvasive prenatal determination of fetal gender.Methods A large scale of clinical implementation was carried out in Southwest Hospital,the Third Military Medical University,Chongqing,China over a 12month period from June,2011 to June,2012.2251 pregnant women referred to outpatient clinic of Southwest hospital were recruited.All of them were ethnic Chinese with singleton pregnancies.Plasma cell free DNA was extracted from 5ml maternal peripheral blood and was prepared for massively parallel sequencing(MPS)by HiSeq2000.Then student t test and the estimation of fetal DNA concentration by sex chromosome are applied to distinguish sex chromosome aneuploidies.Meanwhile,fetal gender was classified by the representation of DNA from chromosome Y for all the samples before getting karyotyping results and follow-up results.Results In MPSbased noninvasive prenatal aneuploidy test,we totally detected out 46 cases with high risk of sex chromosome aneuploidy from all 2251 pregnant women(Positive Rate,2.04%).Among them,7 were tested out as high risk ofXO,5 of them were performed invasive procedure and 2 of them is confirmed,with a PPV(Positive Prediction Value)40.00%;9 cases as high risk ofXXX,6 of them were with karyotyping result and all of them were confirmed to be XXX with a PPV 100%(one of these cases is confirmed to be maternal XXX);Still there are 8 cases we reported as high risk of XXY,7 of them performed karyotyping testing,but only 3 of them is confirmed to be true XXY with a PPV 42.86%;We only detected out 3 XYY cases and 1 of them had accepted amniocentesis which is confirmed to be XYY already;In our earlier clinical application,we reported out 19 non-specific sex chromosome aneuploidy cases(with chromosome Y representation and with lower representation of chromosome X),but only one of them is confirmed to be 45,X,[16]/46,XY,[16] by amniocentesis and other 18 cases confirmed to be false positive with a PPV only 5.26% which showed this non-specific type is of poor prediction power and maybe unsuitable for reporting out in the future.In the gender classification analysis,1669 out of 1683 samples with confirmed gender information of kayotyping result or follow-up result was accurately classified(accuracy rate,99.17%).Conclusion:Our data demonstrates MPS-based noninvasive prenatal testing is an effective way to distinguish sex chromosome aneuploidies and could provide an outstanding additional support to genetic counseling.