OBJECTIVES: To assess use of resources and costs of the surgical versus clinical treatment for obese patients with comorbidities, under the Brazilian private health care system. METHODS: In order to estimate the differences of resource use and costs related to surgery versus clinical treatment one panel of specialists  was conducted to raise up the resources necessaries for the treatment from pre-operatory evaluation to the last medical visit  after 5 years. For the clinical treatment group we assumed a conservative scenario where the complications are not considered. A micro costing technique based on public price lists was applied to value the resources from the panel considering only direct medical costs. A discount rate of 5% was assumed. RESULTS: For the first year the total costs per patient for the surgically treated group were R$14,547, for the open approach and R$31,415 for the laparoscopic approach (pre-operatory assessment R$2,009, inpatient costs R$2,728 versus R$2,493, procedure R$7,233 versus R$24,478, complications R$323 versus R$181 and the clinical follow up R$2,254 for both) and for the clinical treated group the total costs per patient was R$7,545 where R$5,062 occurred due to the obesity management (diet, consults, and drugs for weight management) and R$2,488 for comorbidities (drugs, consults and exams for Diabetes TII, hypertension and hypercholesterolemia). After the first year the surgically treated group had R$1690 of annually costs for the follow up versus R$3290 for the clinical treatment group. After 5 years the total costs were R$22,284 and R$39,153 for open and laparoscopic surgery and R$19,217 for the clinical treatment. CONCLUSIONS: Findings suggest that gastric bypass can reduce the use of resources and costs related to the management of obese patients, under the Brazilian private health care system.