There has been a lack of research regarding endometrial stem cells in farm animals, and particularly, regarding epithelial stem/progenitor cells. We aimed to identify potential stem cell subpopulations in porcine and bovine endometrium by measuring the expression of selected stem cell markers (OCT3/4, CD44, SSEA-1, SOX10, CD73, and CD117) during the follicular and luteal phases of the oestrous cycle. We studied 28 endometrial tissue samples collected from 14 healthy, cycling pigs and cows. The endometrial mucosa of each sample was divided into basal, middle, and luminal portions, and the immunohistochemical staining intensity and percentages of cells that were marker-positive were recorded for each portion of the endometrium. Expression of OCT-3/4 was identified in the glands and stroma, and that of SOX10 and CD117 was identified in stroma of both porcine and bovine endometrium. In porcine endometrium, CD44 was only expressed in the glands, whereas SSEA-1 was expressed in the glands and stroma. In bovine endometrium, CD73 was only expressed in the glands. Differences in the expression of most of these markers were found between phases of the oestrous cycle and/or portions of the endometrial mucosa. Our data indicate the existence of both epithelial and mesenchymal stem cell subpopulations in the endometrium of pigs and cows during their oestrous cycles. The expression pattern of the stem cell marker SSEA-1 in porcine endometrium suggests a possible alternative location of the epithelial stem/progenitor cell population in the middle portion of the endometrial glands.