OBJECTIVES: To analyze and compare costs of treatment of complicated infections from patients in public and private hospitals  METHODS: A retrospective (2008-2009) medical chart analysis was performed in two hospitals in Sao Paulo City, Brazil: Private setting and Public setting. Data from patients over 18 years old with complicated skin/soft tissues infections, complicated abdominal infections and Community Acquired Pneumonia (CAP) were analysed according with type and etiologic agent of infection, antibiotic use as empiric therapy, bacterial resistance environment and  ward or ICU treatment and patients. Total treatment costs were evaluated and expressed in Brazilian local currency (Reais) RESULTS: A total of 50 medical records randomly screened were analyzed, 25 from each hospital. Approximately 34% of each pathology and 32% of patients had ICU hospitalization in both settings. The average cost of private hospital was R$17,072.08 , being 55% due to antibiotics use.  Ceftriaxone was the most used antibiotic as initial therapy,50% of cases.  56% of patients in private hospital had to change antibiotic therapy once at least. In public hospital average cost was R$ 2,051.40 and the antibiotics change remained in the same proportion comparing to the private hospital. Mortality rate was different in Private in Public setting CONCLUSIONS: : The use of appropriate empirical therapy of antibiotic is essential and appears as an important cost driver, mainly to the decision makers who under these total acknowledgement (scientific and economic aspects) could have a useful tool for supply policy interventions. Furthermore combining clinical and cost allows for the best choice of antibiotic use as empirical therapy in these patients