To obtain antibodies specific to desired portions in proteins, synthetic peptides are widely used as immunogens, however, generated antibodies often react improperly with native proteins. Monoclonal antibodies (MoAb), epitopes of which are well defined, would be useful. In this review, we present epitope analysis and its application for immunohistochemical studies on four MoAbs against serum amyloid A(SAA), the serum precursor of fibrillar component in reactive amyloid deposits. Multipin-ELISA (enzyme-linked immunosorbent assay), the epitope mapping system which is based on reactivity with small amount of synthetic peptides immobilized on plastic pins, divided 13 clones of rat-mouse hybrid anti-SAA MoAbs into four. Two were determined epitopes as a portion around residue 18 and 30 of SAA while the other two could not be determined. These epitopes were analyzed using truncated recombinant SAA proteins, which were produced in E. coli, and determined as a portion around residue 90 and 100 (C-terminus), respectively. Negative immunohistochemistry of anti-SAA C-terminus MoAb for human reactive amyloid deposits suggests that SAA C-terminus is removed before or during amyloid deposition.