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Human chorionic gonadotrophin (hCG), a glycohormone widely used in treatment of infertility, is a heterodimer composed of an alpha- and a beta-subunit. The heterodimer could be dissociated during production and storage with an impact on its bioactivity. A CE-SDS method for quantitative analysis of hCG subunit dissociation was established in this study by optimization of a variety of method conditions including sample preparation buffer compositions, incubation temperature, separation voltage, and capillary temperature. This method was validated for good sensitivity, linearity, precision, and accuracy for both α- and β-subunit. CE-SDS also showed much better precision and accuracy than SDS-PAGE. The method was successfully used in both recombinant hCG (r-hCG) produced by cell culture and hCG (u-hCG) derived from urine. The CE-SDS method was used in the study of hCG development and stability. Therefore, it is an useful tool for the quality control of hCG.