To examine whether mucosal cytokine production during remission after resection for Crohn's disease is a predictor of future relapse. Thirty-six patients who remained in remission after resection for terminal ileal or ileo-caecal Crohn's disease were included. At enrollment, blood and mucosal (ileal and rectal biopsies) samples were collected. All patients were followed up regularly for 1 year after enrollment and the disease activity was assessed according to the Crohn's disease activity index. Twenty patients remained in remission and 16 patients relapsed during the 1-year follow-up. Interleukin-1 beta, interleukin-6 and tumour necrosis factor-alpha levels in the ileal mucosa were significantly higher in relapsed patients than in patients in remission. These cytokine levels in the rectal mucosa were not associated with relapse. Conventional blood markers and plasma cytokine levels did not correlate with relapse. Amongst the clinical parameters, a younger age, short disease duration before operation and fistulating disease were risk factors for relapse. In multivariate analysis, only the ileal interleukin-6 level was an independent significant predictor for relapse. The interleukin-6 level in the ileal mucosa during remission after resection for ileal or ileo-caecal Crohn's disease is an independent significant predictor for future relapse.