The present study aimed to investigate faecal calprotectin as a diagnostic marker to differentiate between patients with inflammatory bowel disease (IBD) and those with irritable bowel syndrome (IBS). A total of 20 healthy control subjects, 26 patients with IBS and 58 patients with IBD, including 22 with ulcerative colitis (UC) and 36 with Crohn's disease (CD), were recruited for the present study. Calprotectin was analysed in stool samples, and C-reactive protein (CRP) and the erythrocyte sedimentation rate (ESR) were assessed in blood samples. CRP and calprotectin levels, and the ESR were observed to be significantly higher in patients with CD and UC compared with those of the healthy control subjects (P<0.0001). Furthermore, in patients with IBD and IBS, significant increases in faecal calprotectin and CRP levels were observed (694.8±685.0 µg/g in IBD vs. 85.8±136.1 µg/g in IBS and 0.851±1.200 mg/dl in IBD vs. 0.16±0.23 mg/dl in IBS, respectively; P<0.0001). Area under the receiver operating characteristic curve analysis revealed that, in patients with IBD, the levels of faecal calprotectin [0.931±0.029; 95% confidence interval (CI), 0.874‑0.987] were significantly higher than that of CRP (0.865±0.041; 95% CI, 0.785‑0.946) and the ESR (0.869±0.042; 95% CI, 0.786‑0.952). These findings indicate that faecal calprotectin may represent a novel biomarker for diagnosing IBD and may be effective in distinguishing between IBD and IBS.