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Regulatory T (Treg) cells are specialized immune cells with a pivotal role in the maintenance of immune homeostasis and control of inflammation. However, relatively little is known about immune regulation in the peripheral blood of dogs with primary immune-mediated thrombocytopenia or chronic enteropathy. Using flow cytometry this study investigated Treg responses in the peripheral blood of dogs with respective autoimmune or chronic intestinal diseases and demonstrated that a reduction of Treg frequencies is observed in dogs with clinical signs compared to dogs undergoing remission and healthy dogs. These findings suggest that reduced frequencies of Treg cells in peripheral blood might be causally associated with the onset and/or progression of autoimmune and chronic intestinal diseases in dogs and that measurement of regulatory T cells might represent a useful tool in the monitoring of treatment response and disease progression.