ABSTRACT:The differentiation between inflammatory bowel disease (IBD) and food responsive diarrhea (FRD) is difficult and no objective markers are available. We postulated that patterns of selected key cytokines would help to objectively differentiate between the two subcategories of chronic enteropathies in dogs. We studied mRNA patterns of selected cytokines in dogs with chronic enteropathies. Ten dogs with FRD (= group FRDbef ) and seven dogs with IBD (= group IBDbef ) were presented for endoscopy at the Small Animal Clinic, University of Bern. A control endoscopy was performed in both groups after treatment with an elimination diet for four weeks (FRDaft) or with an elimination diet combined with prednisolone for 10 weeks (IBDaft). Intestinal control samples of gastrointestinally healthy dogs from an independent study were additionally available. Dogs were clinically examined and scored using the canine IBD activity index (CIBDAI). mRNA abundance of interleukin (IL)-5, -10, -12p40, and -13, tumor necrosis factor (TNF)-α, transforming growth factor (TGF)-β1, and interferon (IFN)-γ were analyzed in intestinal samples by reverse transcription and real time polymerase chain reaction. Median CIBDAI decreased in FRDaft (P < 0.01) and IBDaft (P = 0.07) during treatment. In duodenum, IL-12p40 mRNA levels tended to be lower in FRDbef than in IBDbef (P = 0.07). The abundance of TNF-α mRNA was higher in IBDbef than in control dogs (P < 0.05). IL-5 mRNA levels decreased in FRD dogs during treatment (P = 0.06), and IL-10 mRNA levels decreased in IBD dogs (P < 0.05). In colon, IL-5 and IL-12p40 mRNA levels were lower in FRDbef than in IBDbef (P < 0.05) and control dogs (P < 0.01). IL-13 mRNA abundance was lower in FRDbef than in control dogs (P < 0.05) and IFN-γ mRNA abundance was lower in FRD and IBD dogs than in control dogs (P < 0.01). Feeding the elimination diet additionally reduced IFN-γ mRNA levels (P < 0.01), but increased TNF-α mRNA levels (P < 0.05) in FRD dogs. In conclusion, mRNA levels of the selected cytokines before treatment did not show clear differences between FRD and IBD dogs.