Whereas numerous immunoassays have been developed to ensure detection of the entire spectrum of isoforms displayed by the human chorionic gonadotropin (hCG) molecule, significant variation has been demonstrated in how these isoforms are recognized by the antibodies in different immunoassays. The aim of this study was to establish a method using the dual selectivity of the immunoextraction and the mass spectrometry detection for the differentiation between various hCG isoforms in clinically relevant samples. Immunoextraction of endogenous hCG isoforms using a monoclonal antibody (E27) on a 96-well microtitier plate, followed by in-well tryptic digestion, and SIM monitoring of the selected signature peptides, resulted in the qualitative differentiation between several hCG isoforms in serum or urine. We conclude that the orthogonal selectivity conferred by the combination of immunoaffinity extraction and LC-MS analysis offers valuable complementary information to the conventional immunoassays.