Enzymatic and non-enzymatic pretreatments for antigen retrieval (AR) on formalin-fixed, paraffin-embedded, deparaffinised sections were compared and optimised by immunostaining of tissues infected with 13 different pathogens. Enzymatic pretreatment was achieved by incubating slides in 0.25 per cent trypsin (TR) and non-enzymatic pretreatments by heating them in a microwave oven (MWO) or an autoclave (AC). Three different buffers of different pH and molarity including phosphate buffer (PB), citrate buffer (CB) and acetate buffer (AB) were used as AR solutions. All of them were effective regardless of molarity, for the MWO with a processing time of 20 minutes, and the AC with a processing time of 15 minutes. The detectability of many viral antigens was significantly improved by MWO or TR pretreatment, but that of most bacterial antigens was not improved and that of some viral antigens was decreased by TR pretreatment. These results suggest that AR pretreatment is a prerequisite procedure for immunohistochemical detection of many infectious agents but the optimal pretreatment has to be individualised for each agent.