Paneth cells, granule-containing cells located at the bottom of the intestinal crypts, have a role in innate mucosal immunity. We identified the exclusive expression of granulocyte-macrophage colony-stimulating factor (GM-CSF) in Paneth cells using single-cell reverse transcription-polymerase chain reaction and cDNA array. Cytosolic total RNA was aspirated from single Paneth cells and other villous epithelial cells (non-Paneth cells) of rats using capillary micropipettes. In addition to lysozyme, secretory phospholipase A2, defensin, TNF-alpha, and xanthine dehydrogenase genes, cDNA array analysis revealed that the GM-CSF gene is specifically present in Paneth cells, whereas GM-CSF receptor beta-chain mRNA is expressed in Paneth cells and other epithelial cells. There was intense immunohistochemical staining of GM-CSF in Paneth cells but not in other epithelial cells. Treatment of IEC6 cells with GM-CSF enhanced expression of CD80 and CD86. Thus, GM-CSF in Paneth cells might have an important role in mucosal immunity through increasing the expression of costimulatory molecules in epithelial cells.