OBJECTIVES: This research aims to verify the total costs of the medicines that are dispensed by pharmacies of the Brazilian Public Health System (SUS) and that are also part of the Aqui tem Farmácia Popular program (PAFP). This program is characterized by the powerful link between the government and the private pharmacies which provide medicines for free or by co-payment for the population. This work also seeks to draft a comparative analysis between the two distribution forms of the drugs.  METHODS: The direct cost was obtained from the amounts showed on the county purchase invoices.  The indirect cost was identified as a result of a field survey. The sampling selection of visited counties was based on a - non- probabilistic - scenario analysis approach from quality criteria and distributed in each of the five country´s regions. Collection was performed by completing a semi-structured spreadsheet, by documentary analysis and by participant observation. Data collected correspond to the expenses incurred during 2011.  RESULTS: The value of the medicines bought by a private pharmacy it is significantly higher than the one paid by the SUS pharmacy. It is considered as possible explanations of differential of the direct cost between two purchases origins some additional elements that elevate the cost of the private pharmacy regarding the one from SUS:  purchases volume, purchase frequency, presentation, additional costs as logistics, type of packing, costs related to the certification of good production practices. CONCLUSIONS: From the comparative analysis of the SUS pharmacy total cost with the value funded by the Ministry of Health for PAFP medicines, it was possible drawing a comparative with the analyses provided in the National Accounts Tribunal (TCU) audit report. It was observed that the variance shown in the TCU audit report indicates a significant difference between the assessed results in this demonstrative.