Objective: To investigate the value of karyotype analysis, bacterial artificial chromosomes-on-beads (BoBs), chromosome microarray analysis (CMA) and fluorescence in situ hybridization (FISH) in the diagnosis of sex chromosome numerical and structural abnormalities. Methods: Conventional G-banding staining technique was used to analyze the karyotypes of amniotic fluid cells and parental peripheral blood cells in two pregnancies with prenatal diagnosis indications. Sex chromosome numerical and structural abnormalities were analyzed based on the results of G-banding, BoBs, CMA and FISH. Results: The results of G-banding karyotype analysis showed that there were mosaics in amniotic fluid cells collected from both cases. Karyotype of Case A was 45,X[25]/46,X,idic(Y)(q11.2?)[6], and Case B was 45,X[39]/46,X,psu idic(X)(q21.32?)[44]. Parental peripheral blood karyotypes of both families were normal. Prenatal BoBs indicated copy number abnormalities in sex chromosomes (Y chromosome in Case A and X chromosome in Case B). CMA results suggested a 20.1 Mb duplication in Yp11.32q11.222, and a 7.7 Mb deletion in Yq11.222q11.23 in fetus A with possible karyotype of 46,X,idic(Y)(q11.222); for fetus B, a 92.0 Mb duplication in Xp22.33q21.32, and a 63.0 Mb deletion in Xq21.32q28 were detected, and the karyotype might be 46,X,psu idic(X)(q21.32). The mid-term FISH test of amniotic fluid cells showed that 90% of the amniotic cells from Case A were 45,X, and 10% were 46,X,idic(Y)(q11.2); about 38% were 45,X, and 62% were 46,X,psu dic(X)(q21.3) from Case B. Conclusions Numerical and structural abnormalities of sex chromosomes could be accurately diagnosed by combination of several methods including G-banding karyotype analysis, prenatal BoBs, CMA and FISH, which would help to effectively reduce birth defects.