Objective:To develop an unnatural amino acid-labelled HiD-Hin47 fusion protein as a novel carrier.Methods:Twenty versions of the fusion protein were designed, each of which contained a different amino acid site replaced by an azide-bearing amino acid, N6-(2-azidoethoxy) (carbonyl)-L-Lysine (NAEK). These fusion proteins were constructed, expressed and purified, and the yield were evaluated by SDS-PAGE. Based on the highest protein yield, which was approximately 70% of the wild-type yield, the fusion protein with the unnatural amino acid in E677 site was selected. The pneumococcal polysaccharides of serotype 3 (F3) and serotype 6B (F6B) were coupled to the selected fusion protein through a "click" reaction. The conjugates were purified and compared in animal studies with other F3 and F6B conjugates that were coupled to CRM197, tetanus toxoid (TT) and HiD by conventional methods.Results:The immunogenicity of F3 conjugate using HiD-Hin47 as carrier (F3-HiD-Hin47) was slightly better than that of other F3 conjugates. F6B-HiD-Hin47 was significantly better than F6B-TT and F6B-HiD in terms of immunogenicity, but showed no significant difference with F6B-CRM197.Conclusions:NAEK-labelled HiD-Hin47 had the potential as a carrier for pneumococcal polysaccharide conjugate vaccine and was worthy of further study.