Introduction: Microscopic colitis (MC), comprising subtypes of collagenous (CC) and lymphocytic colitis (LC), is characterised by chronic watery diarrhea and normal colonoscopy findings. So far, there have been no data on the incidence or clinical and demographic features of patients with microscopic colitis in Slovenia. Aims and methods: The aim of our study was to determine the incidence of MC, analyze patient demographics, risk factors, natural course and treatment of MC. Data were collected from the medical records of all patients with MC. Results: In the period from June 2009 to October 2011, MC was diagnosed in 27 patients (16 patients with CC, 7 with LC and 4 with mixed form). There were 19 women (70.4 %) and 8 men (29.6 %), their mean age was 54.4 years (range 29–79 years). The annual incidence rate of MC was 10/100,000. Lactose intolerance was diagnosed in nine out of fourteen tested patients (64.3 %). Ten patients (37 %) used diclofenac prior to the onset of symptoms. There was no difference in clinical presentation between patients with collagenous and lymphocytic colitis. MC was incidental histologic report in 3 asymptomatic patients. Currently, 19 patients are without any symptoms, 2 patients still have problems with diarrhea, 2 patients died from other diseases and one patient has been lost to follow-up. Conclusion: The results of our retrospective study show mild clinical course in patients with MC. Discontinuation of diclofenac and loperamide is often sufficient for clinical improvement.