Background and Objective: Inflammatory bowel disease (IBD) should be suspected in any patient presenting with chronic abdominal pain and diarrhea and with histological sampling for further diagnosis. The purpose of this study was to identify patients with inflammatory bowel disease by measuring fecal calprotectin.Materials and Methods: This case- control study was conducted in the Shahid Mohammadi, hospital, in Hormozgan in 2013-2014. One hundred and twenty patients were enrolled, of which 60 were with IBD and 60 patients with IBS. FCP, ESR, Hct and CRP variables were measured in all patients. In order to compare FCP in the understudy and multiple groups, Mann- Whitney and Kruskal- wallis tests were used and one- sample t- test and ANOVA were used to compare the other indexes.Results: According to the results of this study, there were significant differences between the two groups of IBD and IBS in terms of FCP (p<0.05), ESR (p<0.05), CPR (p<0.05), and Hct (p<0.05) variables. So that, the means of FCP, ESR, and CPR were significantly higher in IBD than IBS but the mean of Hct was higher in IBS. At a cut off value of 77.05 units, fecal calprotectin had a sensitivity of 96.7% and a specificity of 91.7%Conclusion: Currently endoscopy and sample- taking are used for the disease activity evaluation but fecal calprotectin measuring appears to be well related to the disease activity and can be a clinically useful non- invasive marker in differentiating IBD from IBS.