Whereas butyrate is well known to induce apoptosis in transformed colon cells in vitro, evidence exists that it inhibits apoptosis of colon crypt cells in vivo. In this study, pigs were fed with resistant potato starch to increase microbial butyrate formation in the colon and to investigate its effects on mitosis and apoptosis. In addition, apoptosis regulating proteins were determined by immunocytochemistry, such as proapoptotic Bak, antiapoptotic Bcl-2, and the epidermal growth factor (EGF), which is synthesized by goblet cells and functions as a survival factor. Two groups of 6 barrows were both supplied with 381 g crude protein and 31 MJ metabolizable energy (ME) daily over a 19-day experimental period. The rations differed in the carbohydrate composition. The controls received gelatinized starch as the main carbohydrate, whereas the experimental group (butyrate group) received a ration with raw potato starch (low ileal digestibility). In the feces, butyrate concentration and pH were monitored daily. After killing the pigs, colon tissue was obtained for histologic and immunocytochemical evaluation, which was performed separately in the luminal, middle, and stem cell compartment of the crypts. In the butyrate group, the total number of apoptotic cells was reduced by 34% (P< or =.001) compared with controls, whereas the mitotic rate was not altered. The crypt depth was only moderately increased by 15%. Apoptosis in the luminal compartment of the butyrate group was reduced by 18.8%, but was increased by 21.7% in the stem cell compartment. The effect of butyrate on apoptosis was paralleled by an increased number of Bcl-2 positive cells mainly in the luminal compartment (butyrate: 2.6 cells; controls: 1.2 cells, P< or =.001), which was more pronounced compared with the number of Bak positive cells in the same compartment. Bak activity in the stem cell compartment was 3.4-fold increased compared with controls (P< or =.001). The size of EGF-positive stained mucus-droplets from the goblet cells was increased in the butyrate group (P< or =.001). We conclude that butyrate inhibits apoptosis of colonocytes in vivo. An excessive proliferation of crypts is counteracted by a shift of the remaining apoptosis towards the stem cell compartment.