Background: Estrogen deficiency affects the structure and function of the salivary glands in women, leading to a decrease in salivary secretion and a change in the composition of saliva. Previous studies on changes in the salivary glands that cause estrogen deficiency have reported only partial results for the parotid and submandibular glands, and there are few comparative morphological studies of histological changes between the parotid and submandibular glands in ovariectomized rats (OVX) leading to estrogen deficiency. This study aimed to analyze the histopathological and histochemical changes in the parotid and submandibular salivary glands causing estrogen deficiency by using OVX, and to discuss the mechanism on these changes. Methods: The parotid and submandibular glands from sacrificed control and OVX groups were fixed with cold 4% paraformaldehyde in phosphate buffer (pH 7.2). The tissues were dehydrated using a series of graded ethyl alcohol and embedded in paraffin. For histopathological analysis, sections cut to a thickness of 6 to 7 μm were stained with hematoxylin and eosin (H&E). For histochemical analysis, Periodic acid-Schiff (PAS), Alcian blue (AB, pH 2.5), and PAS+AB (pH 2.5 and pH 1) staining was performed. Results: Histopathological analysis of OVX tissue showed that the parotid and submandibular salivary glands were broadly and clearly separated and divided into lobes. In OVX, acinar and ductal cells with condensed polymorphic or pyknotic nucleus, which are presumed to be characteristic of apoptotic cells, and degenerated cells with lipid deposition in cytoplasmic granules and ruptured membranes were increased. Histochemical analysis of OVX, confirmed an increase in the number and acidification of acinar secretory granules. Conclusion Histopathological and histochemical changes and the effects of estrogen deficiency are more evident in the submandibular salivary gland than in the parotid gland.