AbstractWe applied native chemical ligation (NCL) method to the synthesis of highly pure lipid‐core peptide (LCP) vaccines to attach various peptide epitopes. In the case of the synthesis of LCP vaccine with two different peptide epitopes, LCP moieties having two free Cys and two protected Cys derivatives (S‐acetamidemethyl‐Cys, (Cys(Acm)), N‐methylsulfonylethyloxycarbonyl‐Cys (Msc‐Cys), or 1,3‐thiazolidine‐4‐carboxylic acid (Thz)) on oligolysine branches were prepared in order to couple two different epitopes by stepwise NCL. It was found that the difficulty in NCL of first two peptide antigen was associated with the steric hindrance. Using Thz instead of Cys(Acm) and Msc‐Cys was important to reduce the steric hindrance and improve NCL yield. © 2008 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 90: 624–632, 2008.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com