Serum amyloid A (SAA) is the major apolipoprotein of high-density lipoproteins (HDL) present during the acute-phase reaction. To map specific epitopes on purified, lipid-free SAA, sequence-specific antibodies raised against synthetic peptides corresponding to amino acid residues 1-17, 14-30, 27-44, 40-63, 59-72, 68-84, 79-94 and 89-104 of human SAA1 were studied. Using the indirect sandwich dissociation-enhanced lanthanide fluorescence immunoassay, antibodies raised against epitopes comprising residues 1-17, 14-30, 40-63 and 79-94 failed to recognize the corresponding domains on isolated human SAA1/SAA2 or a mixture of both isoforms, indicating that these epitopes are masked, apparently because of specific folding and/or self-aggregation (dimerization). The accessible antigenic determinants of isolated SAA are epitopes comprising residues 31-39, 64-78 and 95-104. The present findings indicate that: (i) the same epitopes are exposed, irrespective whether SAA is HDL-associated or in its lipid-free form and that (ii) monomeric and dimeric SAA co-exist to a similar extent in the lipid-free form, irrespective of whether conditions are non-denaturating, denaturating, acidic or basic. From our studies it is proposed that isolated, purified SAA may serve as a reliable standard for quantification of HDL-associated SAA and for mimicking the interaction of acute-phase HDL particles with peripheral tissues in vitro.