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Functional Dyspepsia (FD) as a psychosomatic disorder is an upper gastrointestinal tract disease without organic pathogenesis causes. The psychopathological nature of this disease and its high correlation with anxiety and depression implies the need for psychological interventions. The purpose of the present study is to compare the efficacy of Metacognitive Therapy (MCT) and medication for the symptoms of anxiety, depression, and difficulties in emotion regulation in patients with FD. In a randomized clinical trial, 65 patients with FD