Abstract - Background: Calprotectin is consisting of a protein binding zinc and calcium mainly found in Neutrophils. It is generally associated with inflammation. Elevated fecal Calprotectin can be detected when there is gastric or colorectal malignancy, or when there is an inflammation such as in inflammatory bowel disease (Crohn's disease and ulcerative colitis). Objectives: To assess the role of fecal Calprotectin as an indicator for inflammatory bowel disease and malignancy in chronic diarrhea. Methodology: Cross-sectional study conducted in Al-Sadr Teaching Hospital from January till the end of March 2020, and included (100) patients with chronic diarrhea who underwent fecal Calprotectin test and colonoscopy. Results: Mean age of participants was (36.61 ± 13.09) years, with equal gender distribution. Comparison of fecal Calprotectin level among colonoscopy findings was performed using ANOVA test. There was significant association between the two variables (FCP and colonoscopy finding), P-value < 0.001. In Crohn's disease, fecal Calprotectin level was significantly higher than that of normal group, with a mean difference of (44.53) µg/g, P-value < 0.001. Similarly, ulcerative colitis had significantly higher fecal Calprotectin level than normal group with mean difference of (54.29) µg/g, P-value < 0.001. Conclusions: This study concludes that the level of fecal Calprotectin increases significantly in patients with inflammatory bowel disease and colon malignancy, and can be used to predict the abnormal findings in colonoscopy. However, this indicator cannot discriminate between ulcerative colitis and Crohn's disease.