Objective To explore the clinical value of fecal calprotectin (FCP) in peptic ulcer (PU) as an non-invasive indicator of disease activity compared with gastroscope. Methods The study was conducted in 62 patients with PU confirmed by endoscopy ( PU group) and 30 subjects with normal findings under endoscopy ( control group). Fecal sample ( weight 5-10 g) was collected within 3 days after endoscopy and FCP was measured by emzyme-linked immunosorbent assay (ELISA). The case history and clinical data were collected as well. Results The level of FCP in PU group was significantly higher than that in control group ( 154. 72 μg/g vs. 25. 18 μg/g, P < 0.001 ). In patients with PU at active stage ( n = 32), the level of FCP was significantly higher than that at scar stage (n =30,318.34 μg/g vs. 54. 10 μg/g, P <0. 01 ), and that in control group (25.18 μg/g, P <0.01), while there was no significant difference in FCP between the latter two groups ( P >0. 05 ). The level of FCP had no significant correlation with the location, size or number of the ulcer. Among patients in PU group, the level of FCP in patients presented with haematemesis or melena ( n = 20) was significantly higher than that in patients presented with other symptoms ( n = 42, 1257. 41 μg/g vs. 92. 77 μg/g, P < 0. 01 ). Conclusion The level of FCP is closely correlated with the activity of PU, which is significantly higher at active stage than that at scar stage, as well as in PU patients with bleeding than those without. Measurement of FCP is a convenient and noninvasive method with well compliance of patients, which might be used as an indicator of disease activity in PU.