The backlog in processing patent applications in Brazil has persisted since the enactment of Law 9,279/1996, when the country resumed granting patents on drugs. The agencies responsible for granting such patents, namely the Brazilian National Patent and Trademark Office (INPI) and the Brazilian National Health Surveillance Agency (Anvisa) cite technical and administrative reasons for the backlog. However, little research has focused on the economic impacts for health due to the inefficiency of the Brazilian patent system. The current study thus proposes a methodology to estimate the extent to which government procurement of medicines is burdened by the backlog in drug patent applications. According to the results, a total of more than BRL 14 million (USD 4.5 million) is spent unnecessarily per year by the Federal Government on just one antiretroviral drug due to the extension of the respective patent's life. Measures to resolve this situation are urgently needed in the three branches of government. These include hiring more staff for the INPI, analysis of bills of law under review in the two houses of the Brazilian Congress to amend the Industrial Property Law, and ruling on direct class action claims of unconstitutionality to suppress the legal mechanisms that allow extending the life of patents.