The amino acid sequence of a segment of 106 residues of C4d has been determined by automated sequence analysis of fragments obtained by CNBr cleavage and enzymic digestion with trypsin. Polymorphism has been detected at 3 positions. Residues 9 and 12 are either valine and leucine or alanine and arginine, respectively. Residue 102 is either valine or arginine. When comparing the protein sequence with the nucleic, acid sequence [Carroll, M. and Porter, R.R. (1983) Proc. Natl. Acad. Sci. USA 80, in press] alanine or serine are found at position 98. These results may in part help to explain the inherited variants of human C4 seen on gel electrophoresis.