Background: Colonic mucosa has a high turnover rate. At the end of their lifespan, colonocytes become senescent and die. Histological studies indicate that senescent colonocytes are shed (exfoliated) into the fecal stream in rats, but phagocytosed by mucosal macrophages in humans. We study whether quantification of host DNA in feces can be used as a non-invasive marker for this differential disposal of colonocytes. Methods: Selective primers and probes for the rat and human β-globin genes were designed and used in real-time PCR reactions. Results: Host DNA was quantitatively extracted and detected in fecal samples of both species. Feces of rats fed a humanized diet contained approximately 100 μg rat DNA per g freeze-dried feces. In human feces, however, only 5 out of 12 samples contained detectable, though very low (less than 0.35 μg/g), levels of host DNA. This about 300-fold difference could not be attributed to differences in DNase activities in the fecal stream. Conclusion: Our results indicate that there is considerable luminal shedding of senescent colonocytes in rats, whereas mucosal phagocytosis is the main route of colonocyte disposal in humans. Thus, real-time PCR of host DNA in feces can be applied as a non-invasive method for studying the differential exfoliation of colonocytes.