A stretch of 14 amino acids (542-555) (MCW-1) in the NC16A domain of BP180 has been shown to be an immunogenic and pathogenic epitope for bullous pemphigoid (BP). Therefore, it provides an excellent target for treatment through a complementary peptide approach, which has been established in other autoimmune diseases, including experimental autoimmune myasthenia gravis. We examined two synthetic complementary peptides BP3CP5 and BP5CP3 against this region. These peptides were derived, respectively, by reading the antisense RNA of this region of BP180 in 3'-5' and 5'-3' directions. We found evident complementarities in hydropathic scores between MCW-1 and both complementary peptides. However, by enzyme-linked immunosorbent assay (ELISA), the complementary peptides BP3CP5 and BP5CP3 did not bind to either synthetic peptide BPNP or glutathione-S-transferase (GST) fusion proteins BP180NC16a and GST-BP-1050. BPNP, BP180NC16a and GST-BP-1050 cover the MCW-1 region of BP180 and were used as the natural peptides in this study. In addition, neither BP3CP5 nor BP5CP3 blocked the reaction between BPNP and anti-BPNP antibody, nor did they block immunofluorescent staining of the basement membrane zone by BP sera. Pre-incubation with BP3CP5 and BP5CP3 did not block the binding of BP sera to the BP18NC16a fusion protein in immunoblotting. Furthermore, rabbit antisera raised against BP3CP5 and BP5CP3 did not bind BP sera in ELISA. Pre-incubation with these rabbit antisera did not inhibit or reduce the binding of BP sera to the autoanltigen in either imnmunoblotting or immunofluorescence. Thus, we concluded that complementary peptides against this particular epitope in BP180 NC16A domain showed no specificity as vaccines to BP, although this approach should be tried for other epitopes in various autoimmune bullous diseases.