The current study evaluates the expression of estrogen receptor-alpha (ER-alpha) protein in the digestive tract and other organs using immunohistochemistry in male and female intact rats. As a result, the expression of ER-alpha protein was intensively immunoreactive in the nuclei of squamous epithelium of the forestomach connected to the limiting ridge and the anus connected to the anorectal junction. Rat ER-alpha mRNA signals were also detected in the epithelium of the limiting ridge using in situ hybridization. The incidence of ER-alpha protein in the limiting ridge decreased with age in both males and females. The incidence of ER-alpha protein in the anorectal junction strongly decreased with age in males, although the incidence did not decrease with age in females. In conclusion, it was suggested that estrogen may be involved in the proliferation and differentiation of these cells in the limiting ridge of the stomach and anorectal junction of rats.