Abstract Human C4b-binding protein (C4BP) is an important regulator of the complement system that also binds and inactivates the anticoagulant vitamin K-dependent protein S. These two activities are performed by two distinct polypeptides of 70 kDa and 45 kDa known as alpha- and beta-chains, respectively. C4BP is present in plasma in various isoforms with different alpha beta composition. Here we report multiple discrete variations of the relative levels of the C4BP isoforms among normal individuals and provide evidence that they are determined by genetic factors that segregate with the regulator of complement activation gene cluster. We also report the characterization of the C4BP molecules secreted by HepG2 and Hep3B cells, as well as transfection experiments in COS cells, to illustrate that the relative levels of expression of the C4BPA and C4BPB genes play a major role in determining the proportion in which the different C4BP isoforms are synthesized. Altogether, the data indicate that the human C4BP isoform pattern is genetically determined, but can be modified by factors with a differential effect on the expression of the C4BPA and C4BPB genes. These observations provide a new way to explore the possible association between elevated levels of C4BP and an increased risk to thromboembolic disorders.