Gastrointestinal involvement in Takayasu Arteritis (TA) requires invasive or expensive diagnostic studies. Instead a fecal biomarker can be used as an initial screening test. In this context, S100A12 is promising as an established biomarker in intestinal inflammation and its role in TA pathogenesis. As such we aimed to test the feasibility of fecal S100A12 as a means of the fecal biomarker in gastrointestinal involvement in TA in this pilot study. Our study population consisted of 30 TA patients and 14 control patients with non-inflammatory arthralgia. Patients with inflammatory or infectious gastrointestinal tract diseases, or used oral antibiotics or NSAIDs for the 3 weeks were excluded. Vasculitis involvements were determined with cross-sectional radiologic studies. TA disease activity was evaluated per Indian Takayasu's Activity Score (2010) criteria and vascular involvements were classified according to Numano classification. ELISA test was used to determine fecal S100A12 levels. Fecal S100A12 levels were higher in TA patients when compared to the controls (37.9 ng/ml vs. 12.5 ng/ml p = 0.038). ESR and CRP levels were also higher in the TA group, however not correlated with fecal S100A12. Among TA patients, fecal S100A12 levels were higher inactive ones with ITAS2010 > 1 (72.9 ng/ml vs. 16.7 ng/ml p = 0.016) correlated with total ITAS2010 scores. (R = 0.52 p = 0.003). TA patients with abdominal symptoms had higher fecal S100A12 levels when compared to the remaining TA population (327.8 ng/ml vs. 28.0 ng/ml p = 0.003). However, fecal S100A12 levels in patients with or without mesenteric vessel involvement did not differ. Fecal S100A12 shows promise as a fecal biomarker to screen intestinal ischemia and inflammatory bowel disease in TA patients.