The small intestinal epithelium is continously renewed through a balance between cell division and cell loss. How this balance is achieved is uncertain. Thus, it is unknown to what extent programmed cell death (PCD) contributes to intestinal epithelial cell loss. We have used a battery of techniques detecting the events associated with PCD in order to better understand its role in the turnover of the intestinal epithelium, including modified double- and triple-staining techniques for simultaneously detecting multiple markers of PCD in individual cells. Only a partial correlation between TUNEL positivity for DNA fragmentation, c-jun phosphorylation on serine-63, positivity for activated caspase-3 and apoptotic morphology was observed. Our results show that DNA fragmentation does not invariable correlate to activation of caspase-3. Moreover, many cells were found to activate caspase-3 early in the process of extrusion, but did not acquire an apoptotic nuclear morphology until late during the extrusion process. These observations show that the lack of consensus between different methods for detecting PCD may be explained both by different timing of appearance of PCD markers and, additionally, by the occurrence of different forms of PCD during the normal turnover of cells on small intestinal villi.