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Surrogate markers of bowel inflammation are increasingly being recognized as important, not only as markers of disease activity in inflammatory bowel disease (IBD) but also to differentiate irritable bowel syndrome (IBS) from IBD. The dimeric M2-isoform of pyruvate kinase (M2-PK) has been reported to be elevated in fecal specimens from colorectal cancer (CA) patients, but its role in IBD is unknown. This study investigated the usefulness of fecal M2-PK in cohorts of patients with IBD, IBS, and CA.Stool samples were obtained for calprotectin and M2-PK measurements in patients with previously diagnosed IBD or new patients being investigated for lower gastrointestinal (GI) symptoms in a UK university hospital. Other investigations were performed as directed by the investigating physician and patients with known IBD were assessed for disease activity by a physician global assessment, Harvey–Bradshaw index (HBI), or endoscopic grading.Fecal M2-PK and calprotectin measurements were obtained for 148 patients: 50 with ulcerative colitis (UC); 31 with Crohn's disease (CD), 43 with irritable bowel syndrome/functional bowel disorders (IBS); 7 with colorectal CA, and 17 with miscellaneous conditions (excluded from the analysis). Median M2-PK values (U/mL) were significantly elevated in UC: 20.0 (95% confidence interval [CI] 5.4–69.0, P < 0.0001), CD: 24.3 (95% CI 6.4–44.0, P < 0.0001), and CA: 7.0 (95% CI 4.3–88.0, P < 0.0006) compared to IBS: 0.1 (95% CI 0.0–3.2). There was a strong linear correlation of M2-PK with calprotectin levels. A predetermined cutoff level of 3.7 U/mL for a normal M2-PK test produced a sensitivity, specificity, and positive predictive value (PPV) of 73%, 74%, and 89%, respectively, for organic disease. Furthermore, M2-PK levels were significantly elevated in active, compared to inactive, disease for CD (30 versus 0.55 U/mL, P < 0.005) and UC (40 versus 1.2 U/mL, P = 0.006), respectively.Fecal M2-PK is elevated in IBD as well as in CA patients and is a sensitive and relatively specific marker for organic GI pathology, with a PPV of 89%. Furthermore, it appears to be a potentially valuable, noninvasive marker of disease activity in IBD.