Aims: To investigate the diagnostic value of fecal calprotectin (FC) determined by a new immunofluorescence assay-fluorescence enzyme immunoassay (FEIA) in patient with inflammatory bowel disease (IBD) or functional bowel disease, compared with the typical ELISA kit. Methods: FC was determined simultaneously by FEIA and an ELISA kit in 26 patients with functional bowel disease and 77 patients with IBD. We compared the difference of FC levels between patients with IBD and patients with functional bowel disease. Receiver operating characteristics curve (ROC) was constructed to obtain the optimal cutoff value of FC for distinguishing IBD from functional bowel disease and the corresponding sensitivity and specificity. Results: The median FC levels of patients with IBD in clinical active stage or clinical remission stage was significantly higher than that of patients with functional bowel disease. The median FC levels of patients with IBD in clinical active stage, IBD in clinical remission stage and functional bowel disease were as follow: 699.91 (346.14 ~ 1647.54) μg/g; 407.36 (121.81 ~ 878.48) μg/g; 39.04 (12.09 ~ 81.04) μg/g when FC was measured by FEIA. The median FC levels were 716.99 (240.42 ~ 1232.53) μg/g; 338.46 (53.08 ~ 692.82) μg/g; 41.44 (11.77 ~ 73.19) μg/g among such above three groups of patients respectively, when FC was measured by ELISA kit. The diagnostic value of IBD with FC determined by FEIA (optimal cutoff = 131.79 μg/g) and ELISA kit (optimal cutoff = 121.85 μg/g) presented an area under the curve of 0.881 and 0.873, respectively. Conclusions: FC determined by FEIA was an accurate surrogate marker to distinguish IBD from functional bowel disease.