OBJECTIVES: To quantify the direct costs (hospitalizations and prescription drugs) of the caring strategies for the Inflammatory Bowel Disease (IBD). METHODS: All cases of the major types of IBD, Crohn's disease (CD) and ulcerative colitis (UC), occurred in Apulia between 2002 and 2006 were in the study. The patients were identified through a record linkage procedure among three different regional health databases. Multivariate Poisson regression accounting for over-dispersion was used to assess the average annual direct costs per person. Results were reported, separately for the two diseases, as Incidence Rate Ratios (IRR) with 95% confidence intervals. RESULTS: The cohort consisted of 2,700 cases of CD and 4902 cases of UC. We estimated the average annual costs per person in patients with CD to be equal to 7,153 Euros for hospitalizations and to €2107 for prescription drugs. In patients with UC the average annual costs per person was of €6317 and €2277 for hospitalizations and prescription drugs, respectively. Surgical to medical DRGs ratio for both diseases was 1:5 and the ATC codes relative to intestinal anti-inflammatory, proton pump inhibition, anti-inflammatory/anti-rheumatic and corticosteroids products, represented the 40% of all prescriptions. Overall, the analyses showed, both for DC and CU, that the Charlson Comorbidity Index (CCI) was the only variable associated with the direct costs i.e. a significant increase in the costs (p-value<0.0001) was found according to the severity of the CCI. In particular, it was noted that a worse clinical condition before disease onset (CCI before index date) was predictive of larger costs especially in the case of UC. CONCLUSIONS: These preliminary results show that this innovative cost estimation, obtained with this carefully controlled use of population wide databases, is a valuable alternative to traditional analyses obtained with ad hoc designed and less representative protocols.