The accumulating knowledge about host–pathogen interactions in infectious diseases shows how the immune system interfaces with pathogens, and thus, helps us in understanding the pathogenesis of diseases and improving their treatment. Purified antigens are indispensable while investigating the immune response in both innate and acquired immunities. It is ideal to use native antigens purified from the host organisms in native conditions that sustain their biological activity completely. However, purification of native antigens, especially on a large scale, is technically difficult and generally time consuming. Purifying protein as a peptide-tagged fusion protein is an effective approach. Purification of a recombinant protein engineered to incorporate a polyhistidine tag at either the carboxyl or amino terminus is an established method, and it can be easily modified to obtain optimal results under different conditions. Heat-shock proteins were highly conserved during evolution and are highly homologous between prokaryotic and eukaryotic cells. Their molecular mimicry might have roles in the pathogenesis of chronic inflammatory diseases. We successfully generated histidine-tagged recombinant heat-shock proteins from the periodontopathogens, Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans. The recombinant proteins allowed us to evaluate the immune response to these antigens in periodontitis patients.