Background: Since the 1990s, treatment of patients with rectal cancer has changed in the Netherlands. Aim of this study was to describe these changes in treatment over time and to evaluate their effects on survival. Methods: All patients in the Netherlands Cancer Registry with invasive primary rectal cancer diagnosed during the period 1989-2006 were selected. The Cochran-Armitage trend test was used to analyse trends in treatment over time. Multivariate relative survival analyses were performed to estimate relative excess risk (RER) of dying. Results: In total, 40,888 patients were diagnosed with rectal cancer during the period 1989-2006. The proportion of patients with stages II and III disease receiving preoperative radiotherapy increased from 1% in the period 1989-1992 to 68% in the period 2004-2006 for younger patients (<75 years) and from 1% to 51% for older patients (≥75 years), whereas the use of postoperative radiotherapy decreased. Administration of chemotherapy to patients with stage IV disease increased over time from 21% to 66% for patients younger than 75 years. Both males and females exhibited an increase in five-year relative survival from 53% to 60%. The highest increase in survival was found for patients with stage III disease. In the multivariate analyses survival improved over time for patients with stages II-IV disease. After adjustment for treatment variables, this improvement remained significant for patients with stages III and IV disease. Conclusions: The changes in therapy for rectal cancer have led to a markedly increased survival. Patients with stage III disease experienced the greatest improvement in survival.