Background: Bowel diseases are very common, most of them are functional not organic in nature but clinicians suffer a lot in differentiating between the two categories especially the management is completely different. The symptoms of functional bowel diseases can be very similar to organic inflammatory bowel diseases like ulcerative colitis. In many cases the definitive diagnosis needs invasive procedures including lower colonoscopy and biopsy for histopathological documentation. Aim of the work: To evaluate the clinical value of fecal calprotectin as a non invasive marker differentiating organic from functional bowel diseases in correlation with endoscopic and histopathological examinations. Subjects and methods: The study included 40 patients, selected to represent 2 groups: group (I) included 20 patients with ulcerative colitis (UC) proved by colonoscopy and histopathology who further subdivided into sub-groups according to activity and site of involvement; and group (II) included 20 patients who had symptoms suggestive of irritable bowel syndrome (IBS) and in whom colonoscopy was found to be normal served as control. All participants were subjected to thorough history taking, physical examination and routine laboratory investigations. Calprotectin in feces was measured using the enzyme-linked immunosorbent assay (ELISA).Results: Fecal calprotectin concentration in the patients with UC was significantly higher than in patients with IBS (Mean values ± SD; 201.7 ± 46.7 μg/g vs, 22.3 ± 10.1 μg/g, P < 0.01). A significant difference was also found in the patients with active UC in comparison to UC patients without sign of activity (Mean values ± SD; 220.2 ± 31.1 μg/g vs, 167.3 ± 23.9 μg/g, P<0.05). The sensitivity of fecal calprotectin at cut off value 195.5 μg/g; as activity marker of UC was 82.2 % while its specificity was 85.7 %., Positive predictive value was 90.1% and negative predictive was 66.6%. Conclusion: Fecal calprotectin can differentiate with great acceptance between organic and functional bowel diseases and can be used as a rational fecal marker for intestinal inflammation in clinical practice. This kind of marker is relatively precise, simple and noninvasive and could give a crude idea about the activity of the lesions.