Small intestinal epithelium is a self-renewing system in which the entire sequence of cell proliferation, differentiation, and removal is coupled to cell migration along the crypt-villus axis. We examined whether dual labeling with different thymidine analogues, 5-bromo-2'-deoxyuridine (BrdU) and 5-ethynyl-2'-deoxyuridine (EdU), can be used to estimate cell migration rates on the villi of small intestines in rats. Rats received a single intraperitoneal injection of BrdU and EdU within a time interval, and signals in tissue sections were examined by immunohistochemistry and the click reaction, respectively. We successfully observed BrdU- and EdU-positive cells on the epithelium with no cross-reaction. In addition, we observed an almost complete overlapping of BrdU- and EdU-positive cells in rats administered simultaneously with BrdU and EdU. By calculating the cell migration rate by dividing the distance between the median cell positions of the distribution of BrdU- and EdU-positive cells by the time between the injection of BrdU and EdU, we estimated approximately 9 and 5m/h for the cell migration rates on the villi in the jejunum and ileum, respectively. We propose that dual labeling with BrdU and EdU within a time interval, followed by detecting with immunohistochemistry and the click reaction, respectively, is useful to estimate accurately the cell migration rate in the intestinal epithelium in a single animal.