Tissue antigenicity represents the main limitation for the use of xenografts in clinical practice. To eliminate xenoantigens and avoid graft rejection in human, decellularization is often used to remove all immunoreactive components from the extracellular matrix (ECM). After decellularization, acellular scaffolds are required to be investigated regarding the presence of antigens, but commonly used detection methods solely focus on known xenoantigens such as alpha Gal (Galα1,3-Galβ1-4GlcNAc-R) or major histocompatibility complex-I (MHC-I). However, there are unknown xenoantigens that escape the standard methods. To evaluate the immunological potential of xenogenic tissues, new in vitro methods need to be developed. Therefore, we established a novel human serum-based approach, including dot blot, Western blot, immunohistochemistry, and enzyme-linked immunosorbent assay (ELISA). With these methods, we analyzed protein extracts and tissue samples of native and decellularized bovine carotid arteries. All methods verified an effective removal of potential immunogens from the ECM through decellularization, and relative quantification with ELISA showed that 99.9% (p < 0.01) of antigenic components were successfully eliminated. We compared our human serum-based methods with commonly used assays for the detection of alpha Gal and MHC-I. Our results showed highly increased sensitivity for xenoantigens using the human serum antibody pool. This novel in vitro detection system allows the direct determination of the immunogenic potential of xenografts and is a vast improvement in comparison to the methods used so far. That way, it is possible to optimize the decellularization process to prevent hyperacute graft rejection in patients.