Aim: In Crohn’s disease, the pathogenesis of anastomotic recurrence has been attributed to impaired blood flow, ileocolonic reflux, narrowed caliber of anastomosis, or stasis of intestinal contents. To reduce the risk of anastomotic recurrence, we designed a new ileocolonic anastomosis, and evaluated by the prospective randomized study. Patients and Methods: Since October 1999, 72 patients underwent intestinal resection and ileocolonic anastomosis for Crohn’s disease. The patients were divided at random into two groups, that is, side-to-side isoperistaltic anastomosis (SSIA) and functional end-to-end anastomosis (FEEA). In SSIA group (N=33), their median age at operation was 28.6 (range 16-54), and postoperative period was 35.3 (2-72) months. Five patients had ileitis, 24 had ileocolitis, and 4 had colitis. Fifteen patients had stricturing disease, 15 had penetrating disease, and 3 had inflammatory disease. In FEEA group (N=39), their median age at operation was 31.7 (15-72), median postoperative follow-up was 21.7(1-67) months. Thirteen patients had ileitis, 24 had ileocolitis, and 2 had colitis. Twenty patients had stricturing disease, 18 had penetrating disease, and one had inflammatory disease. Gender, age at operation, affected sites, disease behavior, postoperative follow-up period were not significantly different between two groups. Procedures: In SSIA, both ends were placed in isoperistaltic manner and full thickness of bowel wall was sutured with continuous running suture using 4-0 PDS. Mesenteric side of cut ends were approximated to antimesenteric side of each other intestine. In anastomosis, diseased segment was avoided and the size of anastomosis was designed as long as 8 cm. In FEEA, both ends were placed parallel in antiperistaltic manner, and anastomosed at antimesenteric sides using linear stapler (GIA80 or PLC75). Results: In SSIA group, early postoperative surgical complication (anastomotic leakage) was noted in only one of these patients. Four patients underwent reoperation for recurrence and in three of them anastomosis was removed. But in none of them anastomotic complication was noted. In FEEA group, there were no early surgical complications. Four patients underwent reoperation, and in three of them anastomotic site was removed. In one of these three patients, fistula formation was identified from FEEA. Conclusion: In short term results, side-to-side isoperistaltic ileocolonic anastomosis was safe procedure and is expected to provide good long-term results.