Macrophages are closely related to various diseases and it is therefore important that the properties of macrophages are adequately evaluated in human diseases and mouse disease models. Immunohistochemistry (IHC) of formalin fixed paraffinembedded (FFPE) samples is a very useful tool for examination of macrophages; however, an adequate IHC protocol is required for the examination of macrophage states. In this study, we assessed various antigen retrieval methods in order to devise the optimal protocols for staining of macrophages with a range of antibodies. Optimum combinations of primary antibodies and antigen retrieval protocols were determined; for example, heat treatment with ethylenediamine tetraacetic acid solution, pH 8.0, was the best procedure for IHC using mouse anti-Iba1 and human anti-CD11b, -CD163, -CD169, -CD204, and -CD206 antibodies. Moreover, we found that the immunoreactivity of sliced tissue sections decreased gradually over time in long term storage but that this immunoreactivity was preserved in storage at -80 o C in a deep freezer. The optimal IHC protocols and storage procedures that were determined in this study should be a useful tool for macrophage research.