Apoptosis is a key factor in the death of organ-specific cells. Developing a clear understanding of the effect that bacterial translocation has on initiating apoptotic pathways that induce multiple organ dysfunction syndrome (MODS) is essential for developing effective treatment modalities. Translocation does not occur naturally and apoptotic pathways remain unclear. The aim of this study is to investigate the effect of bacterial translocation on apoptotic pathways in the spleen, small intestine, colon, liver, and mesenteric lymph nodes (MLN) of rats. We randomly divided 12 healthy Wistar-Albino rats into two groups and induced bacterial translocation in the experiment group by clamping the superior mesenteric arteries (SMA) for comparison of test results to the control group. Samples from both groups were collected under sterile conditions and an inoculation procedure was performed. Caspase 3, 8, 9 and p53 were evaluated by immunohistochemistry, and cell expressions were counted. Klebsiella and E. coli colonies were observed in the bacteria cultures associated with the experiment group. Bacterial translocation-activated caspase 8 and 3 were found in all tissues of the experiment group; however, activated p53 was identified only in the colon and liver and activated caspase 9 was seen in small intestine, mesenteric lymph nodes and liver. We concluded that translocated bacteria stimulated extrinsic and intrinsic signaling pathway in gastrointestinal systems.