OBJECTIVES: Several medicines are available in the Brazilian public health system (SUS) to treat schizophrenia. The Ministry of Health (MoH) and Brazilian states share the responsibility of acquiring the atypical antipsychotics, which have significant impact on the public budget. Here, we present the profile of financial resources allocated in the acquisition of atypical antipsychotics in the SUS. METHODS: Descriptive analysis of expenses with drugs, based on the amount dispensed and acquisition prices in 2011. Data were obtained from MoH databases. For  quetiapine, olanzapine, risperidone and ziprasidone, we assumed the financial resources applied by both states and MoH; for clozapine, we needed to accounted only the MoH resources (current values of 2011; exchange rate: US$1 = R$2.04). RESULTS: In 2011, expenses with atypical antipsychotics (clozapine, quetiapine, olanzapine, risperidone, and ziprasidone) for schizophrenia in Brazil reached to US$195,885,270.68. Of this amount, only US$ R$7,496,366.58 (3.83%) came from states and US$188,388,904.10 (96.17%) from  MoH resources. This value represented 11% of MoH's annual budget for acquisition of high-cost medicines. Olanzapine and quetiapine accounted for nearly 81% of total expenses with atypical antipsychotics  (US$103,763,938.18 and US$55,419,573.97, respectively). The others agents represented lower impacts: US$23,199,945.99 (ziprasidone), US$12,881,256.10 (clozapine) and US$620,556.45 (risperidone). CONCLUSIONS: The data demonstrate the impact of financial resources applied in atypical antipsychotics to treat schizophrenia in SUS. In this scenario, strategies to strengthen the health industrial complex  and to optimize resource allocation, as the current production of olanzapine and quetiapine in public pharmaceutical laboratories, are very desirable.