Abstract This study shows that the main beneficiaries of the Patent Cooperation Treaty (PCT) in three Latin American countries, which adhered to it as a result of the obligations provided for in free trade agreements, have been non-residents rather than local companies and individual inventors. This rebuts the frequently made argument that acceding to the PCT would generate incentives for local innovation and benefit local inventors by boosting their capacity to protect their developments in third countries. In the three countries considered in this study, the number of patents granted increased after accession to the treaty. This points to the risk of an erosion of the countries’ flexibilities in designing and implementing patent policies, as allowed by the TRIPS Agreement, with respect to the standards applied to assess eligibility for patent protection.