Background: Budesonide (Entocort) is effective for the treatment of collagenous colitis. Aim: To assess the long-term outcome of patients after induction of clinical remission by budesonide treatment. Methods: Fifty-one patients with chronic diarrhoea and histologically proven collagenous colitis were enrolled in randomized, placebo-controlled crossover trial using budesonide 9 mg daily for 6 weeks. Patients in clinical remission after either initial or crossover budesonide treatment were followed using standardized questionaires. Clinical relapse was defined as five or more loose stools/day for at least 4 consecutive days. Results: A total of 33 patients achieved clinical remission (85% per-protocol). During a median follow-up of 16 months, clinical relapse occurred in 20 patients (61%), after a median time of 2 weeks (range: 1-104, mean: 10 weeks). Patient age <60 years was identified as a significant risk factor for clinical relapse (OR = 7.4, P = 0.048). Budesonide was used for treatment of clinical relapse in 80% of patients achieving clinical response in all of them. Conclusions: Budesonide is effective in the treatment of collagenous colitis. Clinical relapses may occur in a considerable number of patients, particularly in those <60 years. Treatment of clinical relapse with budesonide appears to be an effective option.