Background Surgical resection is almost inevitable in Crohn's disease. Surgery is usually performed for refractory or complicated disease: no studies appear to have been carried out, so far, to evaluate the potential benefits of performing surgery early in the course of the disease. Aim To compare the long-term course of Crohn's disease following ileo-caecal resection performed at the time of diagnosis ( early surgery) or during the course of the disease ( late surgery). Patients and methods Overall 207 patients with ileo-caecal Crohn's disease at their first resection were reviewed: 83 patients underwent surgery at the time of diagnosis ( early surgery), while 124 underwent surgery 54.2 months ( range 1-438) after diagnosis ( late surgery). The mean follow-up after surgery was 147 months ( range 12-534). The primary endpoint was clinical recurrence, defined as need for corticosteroids for symptomatic disease in the presence of endoscopic and/or radiologic recurrence. Secondary endpoints were need for immunosuppressants and surgical recurrence. Statistical analysis: Kaplan-Meier survival method and Cox proportional hazards regression model. Results Within 10 years after surgery, the cumulative probability of clinical recurrence was significantly lower in the early surgery group ( Log Rank test P = 0.01). A trend was observed regarding the need for immunosuppressants ( P = 0.05). No difference was observed regarding surgical recurrence. At multivariate analysis, early surgery was the only independent variable associated with a reduced risk of clinical recurrence ( Hazard ratio, HR = 0.57; 95% CI 0.35 to 0.92, P = 0.02), but not with need for immunosuppressants and surgical recurrence ( HR = 0.51; 95% CI 0.20 to 1.30, P = 0.15; HR = 0.66; 95% CI 0.33 to 1.35, P = 0.25, respectively). Conclusion Early surgery prolongs clinical remission compared to surgery performed during the course of the disease, but the natural history of disease is not modified.