Background and aims: The clinical course of inflammatory bowel disease is characterised by a succession of relapses and remissions. The aim of our study was to assess whether the predictive value of faecal calprotectin - a non-invasive marker of intestinal inflammation - for clinical relapse is different in ulcerative colitis (UC) and Crohn's disease ( CD). Methods: Seventy nine consecutive patients with a diagnosis of clinically quiescent inflammatory bowel disease ( 38 CD and 41 UC) were followed for 12 months, undergoing regular clinical evaluations and blood tests. A single stool sample was collected at the beginning of the study from each patient and the calprotectin concentration was assessed by a commercially available enzyme linked immunoassay. Results: In CD, median calprotectin values were 220.1 mug/g (95% confidence interval (CI) 21.7 - 418.5) in those patients who relapsed during follow up, and 220.5 mug/g (95% CI 53 - 388) in non-relapsing patients (p = 0.395). In UC, median calprotectin values were 220.6 mug/g ( 95% CI 86 - 355.2) and 67 mug/g (95% CI 15 - 119) in relapsing and non-relapsing patients, respectively (p< 0.0001). The multivariate Cox ( proportional hazard) regression model, after adjustment for possible confounding variables, showed a twofold and 14-fold increase in the relapse risk, respectively, in those patients with CD and UC in clinical remission who had a faecal calprotectin concentration higher than 150 μg/g. Conclusions: Faecal calprotectin proved to be an even stronger predictor of clinical relapse in UC than in CD, which makes the test a promising non-invasive tool for monitoring and optimising therapy.