Transient receptor potential canonical channel 6 (TRPC6) is a non-selective cation channel that is activated by diacylglycerol. It belongs to the TRP superfamily, is expressed in numerous tissues and has been shown to be associated with diseases, such as focal segmental glomerulosclerosis, idiopathic pulmonary arterial hypertension and cardiac hypertrophy. The investigation of the channel in human lymphoid tissues has thus far been limited to mRNA analysis or the western blotting of isolated lymphoid cell lines. The present study aimed to detect the channel in human lymphoid tissue using immunohistochemistry. For this purpose, lymphatic tissues were obtained from body donors. The lymphatic organs analyzed included the lymph nodes, spleen, palatine tonsil, gut-associated lymphoid tissues (ileum and vermiform appendix) and thymus. A total of 102 samples were obtained and processed for hematoxylin and eosin (H&E) staining. The H&E staining method was employed to identify five samples with good morphology. In total, three samples of the palatine tonsil of patients were included. Immunostaining was carried out using a knockout-validated anti-TRPC6 antibody. As shown by the results, using immunohistochemical staining, the presence of TRPC6 was confirmed in all the analyzed lymphatic tissue samples. Lymphocytes in lymph nodes, spleen, palatine tonsil, thymus, and gut-associated lymphatic tissues in ileum and vermiform appendix exhibited a positive staining signal. The follicle-associated epithelium of the palatine tonsil, ileum and appendix also demonstrated staining. Vessels of the lymphatic organs, particularly the trabecular arteries of the spleen, the submucosal vessels of the appendix and ileum, as well as the high endothelial venules in the palatine tonsils and lymphatic vessels of the lymph nodes expressed TRPC6 protein. TRPC6 in follicles may be involved in the immune response. TRPC6 in high endothelial venules suggests a role in leukocyte migration. The role of TRPC6 and other channels of the TRP family in lymphatic organs warrant further investigations to elucidate whether TRP channels are a pharmacological target.