Introduction. To select an appropriate and informative histological method is a very important step in morphological analysis of the digestive organs, one of them being immunohistochemistry. The aim of this paper was to highlight the most effective immunohistochemical markers in addition to the well-known markers used in pathological diagnosis. Materials and methods. We studied sections of the intestine and pancreas of Wistar rats (n=20) and fragments of the human colon obtained during resection surgeries (n=4). We described and analyzed the results of immunohistochemical studies with neuronal and glial marker antibodies and inflammatory cells antibodies. Results. Neural (PGP 9.5 protein, tyrosine hydroxylase, synaptophysin, and serotonin) and glial markers (glial fibrillar acidic protein and S100 protein) enable for identifying all of the nervous structures in the murine digestive system such as neurons, nerve trunks and bundles, nerve plexuses, and terminals. Macrophage markers (CD68, Iba1) and mast cell marker (mast cell tryptase) can be applied to study the inflammatory process in the intestinal tissue. We described the key features of primary antibodies and fixative agents used in histopathology. Conclusion. We have shown that the described method is a promising assessment technique for histological studies of the intestine and pancreas pathologies. It can be used in diagnosing conditions associated with inflammation and neurodegeneration. Keywords: duodenum, colon, pancreas, rat, human, innervation, inflammation, immunohistochemistry