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To determine the influence of microscopic disease at an anastomosis following intestinal resection for Crohn's disease, 97 patients undergoing 103 resections were reviewed. Most resections (85/103) involved both small and large bowel and were followed by an ileocolic anastomosis. All resection margins were available and were reviewed. In 52 instances there was no evidence of Crohn's disease at the margins. In 51 instances histologie evidence of Crohn's disease varying from chronic inflammation to tissue destruction was present in one or both margins. The incidence of immediate postoperative anastomotic complications (leak with fistula or abscess, or obstruction) was identical in patients with microscopically normal margins (3/52; 6%) and in patients with microscopic Crohn's disease at the margins (3/51; 6%). The patients were followed for a mean of 5.4 ± 4.2 years. A clinical recurrence developed during the follow-up period in 50% (26/52) of those patients with normal margins, and in 61% (31/51) of those patients with involved margins. A suture line recurrence developed in 35% (18/52) and required reoperation in 17% (9/52) of those patients with microscopically normal margins. A suture line recurrence developed in 41% of the patients (21/51) and required reoperation in 24% (12/51) of those with microscopically involved margins. None of these differences are statistically significant. The presence or absence of microscopic disease at the anastomosis did not appear to influence immediate anastomotic wound healing or long-term recurrence rates. We therefore recommend conservative resections for Crohn's disease to achieve grossly uninvolved margins rather than the sacrifice of normal bowel to achieve histologically normal margins.