Inflammatory bowel diseases (IBD) are idiopathic, remitting and relapsing diseases causing chronic inflammation of intestine. Initial diagnosis, assessment of disease activity, and prediction of treatment outcomes present challenges to physicians in clinical care of IBD. Therefore it is critical to accurately determine inflammatory activity of the gut. Endoscopy, the current gold standard for assessing and monitoring intestinal inflammation, is costly, invasive and at times, dangerous. Fecal biomarkers are a simple, reliable, non-invasive test that, because of their direct contact with the intestinal mucosa, may be more accurate in determining intestinal inflammation than serum biomarkers. Since calprotectin was identified as a marker for IBD, several additional fecal markers, including lactoferrin, S100A12, and M2-pyruvate kinase, have been evaluated for their ability to differentiate and monitor disease activity. Fecal biomarkers are useful in differentiating IBD from functional bowel disorders, monitoring response to treatment and predicting clinical and endoscopic relapse. Although they may not ever replace endoscopy, fecal markers could minimize unnecessary, potentially dangerous examinations and help guide IBD management in a more cost-effective manner.