BackgroundDysregulated T lymphocyte response is thought to play a key role in chronic intestinal inflammation (CIE).ObjectivesTo evaluate the presence of changes in peripheral and intestinal T lymphocyte subsets and to describe potential immune and inflammatory biomarkers in dogs with CIE.AnimalsSixteen healthy dogs and 26 dogs were diagnosed with CIE.MethodsProspective case‐control study evaluating peripheral and intestinal T lymphocytes using flow cytometry and inflammatory markers obtained from complete blood cell counts.ResultsDogs with CIE had higher peripheral activated T helper (Th) lymphocytes (87/μL [18‐273] CIE, 44/μL [16‐162] healthy control (HC, P = .013) and regulatory T cells (Treg; 108/μL [2‐257] CIE, 34/μL [1‐114] HC, P = .004). In the intestinal epithelium, CIE dogs presented lower percentages of Th (4.55% [1.75‐18.67] CIE, 8.77% [3.79‐25.03] HC, P = .002), activated Th cells (0.16% [0.02‐0.83] CIE, 0.33% [0.05‐0.57] HC, P = .03) and CD4/CD8 ratio (0.08 [0.02‐0.39] CIE, 0.21 [0.07‐0.85] HC, P = .003). Conversely, higher percentage of activated T cytotoxic cells (20.24% [3.12‐77.12] CIE, 12.32% [1.21‐39.22] HC, P = .04) and interferon‐gamma (IFN‐γ) producing T lymphocytes (7.36% [0.63‐55.83] CIE, 1.44% [0.00‐10.56] HC, P = .01) within the epithelium was observed. In the lamina propria the percentage of Treg lymphocytes was higher (6.02% [1.00‐21.48] CIE, 3.52% [0.18‐10.52] HC, P = .02).Conclusions and Clinical ImportanceSystemic and intestinal immune alterations occur in dogs with CIE suggesting that blood IFN‐γ producing T lymphocytes and the systemic immune‐inflamation index (SII) could potentially serve as biomarkers for the disease.