Objective: It was demostrated that FAS expression increases not only in mucosa involved by active colitis but also in normal mucosa of ulcerative colitis (UC) patients. Our aims were to evaluate the role of FAS expression in differential diagnosis of IBD, to search for any possible change during the progression of the disease in patients with clinical and endoscopic follow-up. Method: Among 82 colonoscopic biopsy samples of 50 UC cases,13 samples were classified as remission,15 as resolution, and 54 as active period;35 samples of 30 Crohn Disease (CD) cases were classified as active period. Fifteen cases with normal endoscopic and morphologic findings comprised the control group. Results: Between UC and CD active periods and control group, a significant difference was found (p=0,0001). There was a statistical correlation between FAS expression of basal crypt of normal mucosa in UC active period and the disease duration (p=0,036). Conclusion: The increasing in FAS expression in patients with IBD can not be explained only by the inflammation. FAS expression can not aid us in the differential diagnosis of UC and CD, but it seems that it is related to the extent of inflammation in UC. The relation between the disease duration and an increase in FAS expression active UC, might have a significant role in carcinogenesis in UC.