Background: Irritable Bowel Syndrome (IBS) is a functional somatic syndrome characterized by patterns of persistent bodily complaints for which a thorough diagnostic workup does not reveal adequate explanatory structural pathology. Detailed insight into disease-specific health-care costs is critical because it co-determines the societal impact of the disease, enables the assessment of cost-effectiveness of existing and new treatments, and facilitates choices in treatment policy. In the present study the aim was, to compare the costs and magnitude of healthcare consumption for patients diagnosed with Irritable Bowel Syndrome (IBS) in primary and secondary care, compare these costs with the average health care expenditure for patients without IBS and describe these costs in further detail. Methods: Reimbursement data for patients diagnosed with IBS by a general practitioner (GP) or specialist between 2006 and 2009 were extracted from a healthcare insurance company and compared to an age and gender matched control group of patients without IBS. Using a case-control design, direct medical costs for GP consultations, specialist care and medication prescriptions were calculated. Results: Data of 326 primary care and 9274 secondary care IBS patients were included in the analysis. For primary care patients, the mean total annual health care costs for the three years after diagnosis compared to the three years before diagnosis, increased with 486 Euro after IBS was diagnosed, whereas for secondary care patients, these costs increased with 2328 Euro. Total health care costs remained higher in the three years after the initial diagnosis when the patient is treated in secondary care, compared to primary care. This increase was significant for hospital specialist costs and medications, but not for GP contacts. For controls, there was no significant difference in mean total annual health costs in the three years before and the three years after the diagnosis and also no significant difference in cost increases between both ...