The purpose of this study was to investigate the structure and secretory function of the von Ebner's gland in parasympathetic or sympathetic nerve innervation. Sprague Dawley rats were sacrificed 3, 7, 10, 14, and 21 days after bilateral glossopharyngeal or hypoglossal nerve axotomy, respectively. The circumvallate papilla portion of the tongue was dissected and we observed morphological changes in the von Ebner's gland. The properties of glycoconjugate in the von Ebner's gland were investigated using nine biotinylated lectins (PSA, UEA I, GSL I B4, ECL, DBA, SBA, HPA, SJA, or sWGA). Compared with the control group, cytoplasmic vacuoles appeared in the serous acini of the von Ebner's gland in the 3-day group, and the serous acini were significantly vacuolized and degenerated in the 10-day group after glossopharyngeal nerve axotomy. However, the structure of the von Ebner's gland did not change after hypoglossal nerve axotomy. In the control group, the von Ebner's glands secreted glycoconjugates containing α-D-galactose, N-acetyl-D-galactosamine, and N-acetyl-D-glucosamine oligomer, and the amount of the secretion decreased significantly in the 10-day group after glossopharyngeal nerve axotomy. However, the amount of the glycoconjugate secretion did not change after hypoglossal nerve axotomy. Therefore, the results of this study suggest that the glossopharyngeal nerve containing parasympathetic nerve fibers is important for maintaining the structure of and secretory function in the von Ebner's gland in rats.