Trade in counterfeit medicines raises serious public health concerns. However, efforts geared towards combating trade in counterfeit medicines tend to focus more on the protection of trademarks, which may not necessarily protect the public from the adverse consequences of using counterfeit medicines. This arises from differences in the meaning of “counterfeit” in the intellectual property and public health contexts. This article analyses the extent to which the anti-counterfeiting legislation and institutions in two African countries, Kenya and South Africa, are capable of combating trade in counterfeit medicines in a manner that protects both the public and brand name owners. The article examines the anti-counterfeiting legislation and institutions that ensure compliance with the standards for marketing medicines that are in place in these countries, in order to draw lessons on how they can be used to balance the protection of public health interests and trademarks.