The treatment goal in Crohn's disease is clinical remission, not complete mucosal healing. The incidence of mucosal inflammation in Crohn's disease patients in clinical remission is not known. Whole gut lavage is an objective method of assessing mucosal inflammation. We aimed to assess levels of mucosal inflammatory activity in a group of patients with clinically inactive Crohn's disease. We prospectively assessed 30 patients with inactive Crohn's disease and 28 controls. Inactive disease was defined as Crohn's disease activity index of less than 150. All underwent whole put lavage, with analysis of whole gut lavage fluid IgG, haemoglobin, interleukin-1 beta, interleukin-8 and granulocyte elastase. Serum inflammatory parameters were collected for comparison. Of the 30 patients with Crohn's disease, 10 (33%) had an abnormal immunoglobulin G, 21 (70%) had an elevated interleukin-1 beta 20 (66%) interleukin-8 and 10 (33%) granulocyte elastase in the whole gut lavage fluid. 58% of patients had either 1 or 2 abnormal results. In contrast only 10% had 1 or 2 abnormal serum results. Few abnormalities were present in lavage fluid or serum of the control population. We concluded that ongoing mucosal inflammation is detectable in whole gut lavage fluid of up to 2/3 of Crohn's disease patients in clinical remission.