BACKGROUND: Incidence rates of microscopic colitis are mainly based on regional data from a limited number of countries. To evaluate geographical differences and changes over time, more nationwide incidence rates are needed. AIMS: The aim of this retrospective study was to assess the incidence rate of microscopic colitis in the Netherlands in a nationwide cohort. METHODS: A search was performed in the Dutch pathology registry, covering records of all approximately 16.5 million inhabitants. Incident cases were defined as a first diagnosis of microscopic colitis (collagenous or lymphocytic colitis) between 2000 and 2012. RESULTS: In total, 7228 incident cases were identified with a mean annual incidence rate of 3.4 per 100,000 person years. Collagenous colitis was present in 3741 cases and lymphocytic colitis in 2718 cases, with a mean annual incidence rate of 1.8 and 1.3 per 100,000 person years, respectively. Remaining 769 cases were described as undefined microscopic colitis. Collagenous and lymphocytic colitis incidence rates increased significantly over time (p<0.001) with a male:female ratio of 1:3 and 1:2, respectively. CONCLUSION: The Dutch mean annual incidence rates of collagenous and lymphocytic colitis were considerably lower than previously reported by other countries. However, incidence rates increased gradually over time, with a clear female predominance.