The S region of the murine major histocompatibility complex (MHC) encodes the structural gene for the fourth complement component (C4) and controls C4 serum levels and expression of the sex-limited protein (Slp). Although Slp was first throught to be an allele of C4, more recent studies have suggested that Slp is either a modified product of the C4 locus or is encoded at a separate locus. By using a sensitive peptide analysis technique, each of the three constitutive polypeptide chains of C4 and Slp was compared, and multiple distinct peptides as well as several shared peptides were detected. These results demonstrate that although C4 and Slp undoubtedly share a common genetic origin, they are encoded by separate structural genes.