Background: A significant association between atopic dermatitis and leaky gut syndrome has been demonstrated in humans. No studies have been conducted to determine whether there is an association between atopic dermatitis and intestinal damage in dogs. Objectives: This study aimed to determine whether there is an association between canine atopic dermatitis and intestinal damage using selected intestinal-related biomarkers. Methods: Twenty-six dogs with atopic dermatitis and 10 healthy dogs were included. Moderate-to-severe pruritus, erythema, erosion and alopecia on different parts of the body were sought in dogs to suspect atopic dermatitis. The presence of atopic dermatitis was confirmed by an allergic skin test. Serum biomarkers including intestinal fatty acid binding protein (I-FABP), intestinal alkaline phosphatase (IAP), trefoil factor-3 (TFF-3), immunoglobulin E (IgE), interleukin-4 (IL-4) and interleukin-13 (IL-13) concentrations were measured from venous blood samples. Results: Of the 26 dogs tested for allergens, 16 were found to be sensitive to mould mites, 10 to vernal grass, eight to house dust mites, five to wheat dust and five to grass pollen mix allergens. Significant increases in serum IAP, TFF-3, IgE, IL-4 and IL-13 concentrations were determined. Conclusion: It was thought that the increase in TFF-3 and IAP concentrations may be due to the presence of intestinal epithelial damage and the repair of this damage. In addition, the development of atopic dermatitis may be predisposed to the entry of allergens into the body through sites of intestinal damage.