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The association of Takayasu's arteritis (TAK) and inflammatory bowel disease (IBD) has previously been reported in case series. Microscopic colitis (MC) has IBD-like symptoms with regard to clinical and histopathological feature. We aim to assess the presence of MC in TAK patients in this study. We cross-sectionally assessed TAK patients, between the ages of 18-65 years, who were diagnosed according to the American College of Rheumatology (ACR) criteria. Disease activity was evaluated by Kerr's criteria. Age- and sex-matched irritable bowel syndrome (IBS) patients were selected as control group. All patients and controls have been interviewed for IBD and IBS symptoms using the questionnaires of WHO guideline and Rome III criteria, respectively. Lower endoscopic procedure was performed with at least five random biopsies taken from different colonic segments and the terminal ileum. A blinded expert pathologist evaluated the specimens for the features of MC. Thirty TAK patients (29 females and 1 male) with the mean age of 35 ± 11 years (range, 20-59 years) and 15 IBS controls with the mean age of 38 ± 13 years were included in the study. TAK patients all fulfilled the MC criteria (three "complete" and six "incomplete" cases). MC was found to be significantly higher in active TAK patients in comparison to inactive group (67 vs 14 %, p = 0.03, OR = 7.9). Our results show that there is an increased frequency of MC in TAK patients, and this is the first report on the association of TAK and MC.