A recently discovered familial lipoprotein disorder is characterized by reduced plasma levels of high density lipoproteins (HDL) and elevated triglyceride levels. The clinical aspects of this disorder are presented in an accompanying article (Franceschini et al. 1980. J. Clin. Invest. 66: 892-900). The apoprotein content of the HDL isolated from these patients differed markedly from that of normal HDL in that three apoprotein bands not previously described in man were present as major protein components. As determined by sodium dodecyl sulfate (SDS) gel electrophoresis, the relative molecular weights (Mr) of these new apoprotein bands were 55,000, 35,000, and 28,000. Although the Mr 28,000 apoprotein coelectrophoresed with authentic A-I on SDS polyacrylamide gels and showed immunochemical identity with the A-I apoprotein when tested with monospecific apo-A-I antiserum, it contained two amino acid residues, cysteine and isoleucine, which were not present in the amino acid sequence of normal human apo-A-I. This variant form of the A-I apoprotein was designated the A-IMilano apoprotein and denoted A-Icys. By virtue of the presence of cysteine (2 mol/mol A-Icys), the A-Icys apoprotein was capable of forming intermolecular disulfide bonds, and dimer formation of A-Icys produced the Mr 55,000 apoprotein. The Mr 35,000 apoprotein was composed of two different subunits, A-Icys and A-II. By analogy to the apo(E--A-II) complex, which also occurs in human HDL, this mixed disulfide complex was designated as the apo(A-Icys--A-II) complex. The A-IMilano (A-Icys) is the first example of a variation in the primary sequence of a protein of plasma lipoproteins.