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Exposure to human serum induces the lysis of xenogeneic cells through natural antibodies and complement activation. The carbohydrate Galactose-α1,3-Galactose (Gal-α1,3-Gal) epitope, has been shown to be the principal antigenic determinant on target cells. This reaction is, therefore, particularly important for xenogeneic cell-based therapy. As a first step toward the evaluation of the impact of this phenomenon for encapsulated xenogeneic cells, we have evaluated the presence of the Gal-α1,3Gal epitope on two cell lines currently being used for the systemic delivery of protein in the periphery or the treatment of neurodegenerative diseases. In the second part of the study, we have tested and compared human serum and cerebrospinal fluid (CSF) for the presence of xenoreactive natural antibodies (XNAs) and their potential impact on the survival of xenogeneic cells. Fluorescence-activated cell sorting analysis indicated that baby hamster kidney (BHK) cells expressed low levels of the α-Gal epitope, whereas mouse myoblast C2C12 cells were extensively stained with the specific IB4-lectin. There was a direct correlation between serum killing and the level of Gal-α1,3-Gal epitope expression on these cells. Importantly, we showed that CSF did not lyse BHK and C2C12 cells as determined by cytotoxic crossmatch assays. The reaction was specific as the addition of soluble Gal-α1,3-Gal sugar to human serum effectively reduced cell killing, and the overproduction of α-1,3-galactosyltransferase in BHK cells significantly increased inactivation by human serum. To interfere with this antibody–antigen reaction and develop cell lines particularly suitable for cell-based therapy, we either selected C2C12 clones expressing low levels of Gal-α1,3-Gal or high levels of α-1,2-fucosyltransferase. These cells were found to be resistant to complement-mediated cytolysis. These strategies may, therefore, protect encapsulated xenogeneic cells transplanted in the periphery or the central nervous system even in an unlikely event of a blood–brain barrier breakage and the post-transplantation development of an antibody response.