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The current knowledge on the histological structure of the gastrointestinal tract (GIT) in cetaceans is based on general descriptions, which do not reflect the diversity of these marine mammals. The aim of this study was to characterize the histology and expression of immune cell markers in samples from the GIT and lymph nodes (LNs) in a harbour porpoise (Phocoena phocoena), which died due to bycatch in the Bay of Biscay, Cantabrian Sea. After hematoxylin-eosin and Masson's trichrome staining, the thickness of the histological layers of the GIT was measured, being greater in the stomachs and anal canal, although no significant differences were found among any intestinal segment (p = 0.448). LNs exhibited a well-differentiated cortical region, containing lymphoid follicles, and a medullary area. In addition, immunohistochemical techniques were performed to identify the following markers: IBA1 for macrophages, CD3 for T lymphocytes, and CD20 for B lymphocytes. The distribution of immune cells varied significantly along the GIT, with higher percentages of all three cell types in the distal intestine and the anal tonsil. Variation in thickness, morphology of the folds, and the presence of Peyer's patches allowed to distinguish the duodenal ampulla and the distal segments from the rest of the intestine. Within the LNs, B lymphocytes represented the predominant cell population. This study establishes a reliable methodology for the characterization of the histological structure of the GIT and associated lymphoid tissue in cetaceans and provides a description of the histological structure of those organs in harbour porpoise, useful for future research studies.