Background: Histopathology is widely used for the diagnosis of inflammatory bowel disease in dogs. Variations in lesions and unavailability of uniform grading systems limit the usefulness of histologic examination. Hypothesis: CD3 cell numbers in chronic enteropathies of dogs correlate with clinical activity of the disease and with severity of histopathologic changes. Animals: Nineteen client‐owned dogs examined because of chronic diarrhea, vomiting, or both. Methods: Samples of duodenal and colonic mucosa were collected endoscopically before and after treatment. Dogs that responded to a hypoallergenic diet were grouped as food‐responsive diarrhea dogs (FRD, n = 10). Dogs with no clinical improvement after 10 days of treatment then received prednisolone (immunosuppressive doses) and were grouped as steroid‐responsive diarrhea dogs (SRD, n = 9). Histopathologic assessment with a standardized grading system was performed retrospectively on the intestinal samples. Histologic score, total number of infiltrating cells, and CD3‐positive cells were counted and compared with the clinical scoring. Results: No statistically significant difference was detected among histologic grading, total number of cells in the lamina propria, and T‐cell numbers in biopsies before and after treatment in either group (FRD and SRD). Conclusions and Clinical Importance: Currently used histopathologic grading scores, total numbers of cells, and numbers of CD3‐positive cells did not allow differentiation between FRD and SRD and did not correlate with clinical response to therapy. Based on these results, new grading scores assessing other criteria than total cell numbers and CD3‐positive cells should be evaluated in the future.