In this study, we investigated the potential molecular and immunological differences resulting from production of the recombinant fusion proteins (Hybrid-1, comprising of the immunodominant antigens Ag85B and ESAT-6 from Mycobacterium tuberculosis) in two different expression systems, namely M. smegmatis and Escherichia coli. The fusion protein was successfully expressed and purified from both bacterial hosts and analyzed for any host-dependent post-translational modifications that might affect the immunogenicity of the antigen. We investigated the immunogenicity from both from E. coli-derived Hybrid-1 fusion and M.smegmatis-derived Hybrid-1 fusion in a murine vaccination model, together with a reference standard Hybrid-1 (expressed in E. coli) from the Statens Serum Institut. No evidence of any post-translation modification was found in the M. smegmatis-derived Hybrid-1 fusion protein, nor were there any significant differences in the T-cell responses obtained to the three antigens analyzed. In conclusion, the Hybrid-1 fusion protein was successfully expressed in a homologous expression system using M. smegmatis and this system is worth considering as a primary source for vaccination trails, as it provided protein of excellent yield, stability and free from lipopolysaccharide.3