The present study attempted to clarify the characteristics of the guttural pouch mucosa in equines and to evaluate its foreign substance clearance ability. The specimens were collected from nine regions (eight in the guttural pouch mucosa, and one in the nasopharynx mucosa). We first examined the pouch mucosa by light and electron microscopy. We then measured the frequency of goblet cells per 200 epithelial cells, the length of the cilia, the thickness of the epithelial cell layer and lamina propria and statistically analyzed the data. The guttural pouch mucosa consisted of stratified columnar epithelia with brush-like cilia, and there were almost no histological differences between adults and foals. The morphometrical study revealed significant differences in goblet cell frequency (p<0.001) and the thickness of lamina propria (p<0.05). By contrast, no statistically significant difference was detected in the length of the cilia or the thickness of the epithelial cell layer. These findings suggest that the guttural pouch mucosa provides foreign substance clearance ability, but that its ability varies among different regions of the epithelium.