Mast cells are highly heterogenic cells meaning that different genes are expressed in each different population of mast cells. So far, it has been very difficult to detect that which individual mast cell expresses which genes in situ. In this study, we amplified the mouse mast cell protease (mmcp)-4 mRNAs by in situ RT-PCR method and successfully visualized the signals of amplicons. It was found that the cells expressing mmcp-4 mRNA were connective tissue type mast cells but not mucosal type mast cells, in mouse tongue and intestine sections. This is the first report that the cells expressing the mast cell-specific gene were detected on histological specimens by in situ RT-PCR method. And it is suggested that this method will be a powerful tool for clarifying the relationships between pathological and physiological changes in diseases and many genes expressed in mast cells.