The aim of this study was to describe the clinical course of Crohn's disease (CD) in a well-defined, homogeneous groups of patients. A total of 480 patients with CD were followed up from diagnosis up to 20 years. Definitions of patient subgroups were made according to the Vienna Classification. Markov chain analysis was used to estimate the probabilities of remissions and relapses during the disease course. Both age at diagnosis and behavior were associated with different disease locations. Patients with ileal disease had a greater need for surgical and a lesser need for immunosuppressive treatment; patients with ileocolonic disease were diagnosed at an earlier age and showed a lower probability of remaining in remission during the disease course; patients with colonic disease needed less surgical or steroid treatments; patients with intestinal penetrating disease were frequently submitted to abdominal surgery, whereas those with anal-penetrating disease often needed immunosuppressive treatment. Approximately 40% of the patients were in clinical remission at any time, but only about 10% maintained a long-term remission free of steroids after their initial presentation. A more benign clinical course could be predicted in patients who stay in remission in the year after diagnosis. The grouping of patients with CD according to the Vienna Classification and/or the clinical activity in the year after diagnosis is useful in predicting the subsequent course of disease.