OBJECTIVES: Because of its long duration, Crohn`s disease (CD) causes high use of health services and high lifetime costs for medical care. The aim of the present study was to measure the annual costs of patients with CD from the Brazilian public heath perspective and to identify potentially relevant determinants of costs. METHODS: Thirty one gastroenterologists from southeast Brazil prospectively evaluated all their CD patients during two months. They used a structured questionnaire specifically developed to evaluate resource use by patients with CD. Costs of medical services (diagnostics and treatment) were considered as well as costs of medication. Resource use was valued using government reimbursement for hospital services and government tender prices for drugs. RESULTS: 221 patients were evaluated. The mean annual cost of one CD patient was R$ 2.239,67, including medication, physician, laboratory, diagnostic procedures, hospitalization and surgery costs. Medication, hospitalization, surgery and laboratory/ diagnostic procedures accounted, respectively for 79%, 18%, 2% and 1% of the total annual costs. Mesalazine was the most used drug to initiate CD`s treatment (59% of the times). Although mesalazine is deemed to be more expensive than sulfasalazine, there was no statistical difference between the costs of the patients treated with mesalazine and sulfasalazine. In fact, due to differences in the mean dosage of theses drugs, mesalazine daily cost is lower than sulfasalazine. CONCLUSION: This is the first time that CD treatment costs have been demonstrated from the Brazilian public health perspective. Considering that there was no statistical difference in total costs among patients taking mesalazine and sulfasalazine, and that medications represent more than 70% of total CD treatment annual costs in the public Brazilian healthcare system, the use of mesalazine may represent a reduction factor in the financial resource expenditure for the treatment of CD.