Three mouse monoclonal antibodies specific for human apolipoprotein (apo) A-I and one specific for human apo-A-II were characterized with respect to their binding of high density lipoprotein (HDL) particles in solution. The apo-A-II-specific antibody bound 85% of 125I-HDL and 100% of soluble 125I-apo-A-II. However, none of the apo-A-I-specific antibodies bound greater than 60% of either HDL or soluble apo-A-I. Technical issues such as limiting amounts of antibody or antigen, radioiodination of the ligands, unavailability of the epitopes for reaction with antibody, selective binding of apo-A-I isoforms, and individual allotypic differences in apo-A-I were not responsible for the observed incomplete binding of all HDL and apo-A-I. The results suggested the existence of intrinsic immunochemical heterogeneity of apo-A-I both as organized on HDL as well as in free apo-A-I in solution. The validity of this observed heterogeneity was supported by demonstrating that (i) increased binding of HDL occurred when each of the apo-A-I antibodies was combined to form an oligoclonal antibody mixture, and (ii) 100% binding of HDL occurred when two apo-A-I antibodies were combined with the single apo-A-II antibody. To understand the basis for the heterogeneity of expression of apo-A-I epitopes on HDL, two hypotheses were examined. The first hypothesis that these apo-A-I antibodies distinguished apo-A-I molecules from different synthetic sources was not substantiated. Two of the antibodies bound epitopes on apo-A-I molecules in both thoracic duct lymph as an enriched source of intestinal HDL and the culture supernatants of the hepatic cell line Hep G2 as a source of hepatic HDL. The second hypothesis that the antibodies identified differences in the expression of apo-A-I on HDL subpopulations that were distinguished on the basis of size or net particle charge, i.e. organizational heterogeneity, appeared to provide the best available explanation for the immunochemical heterogeneity of apo-A-I in HDL. Relative differences in the expression of three distinct apo-A-I epitopes were demonstrated in HDL subpopulations obtained by either density gradient ultracentrifugation or chromatofocusing. In light of these studies, we conclude that there is intrinsic heterogeneity in the expression of intramolecular loci representing the apo-A-I epitopes identified by our monoclonal antibodies. Such heterogeneity must be considered in analysis of the biology and physiology of apo-A-I and lipoprotein particles bearing this chain.