Through its participation in the South African Customs Union (SACU), South Africa has been involved in negotiations with the United States government on the finalization of a free trade agreement (FTA). Although the US-SACU negotiations eventually ground to a halt, they are more than likely to be reinstated some time soon, and the farreaching implications they portend will have to be confronted afresh. The concern of this contribution is the effect of the US insistence on stronger intellectual property protection for pharmaceutical patents in these bilateral agreements, the resultant impact on the prices of medicines for life-threatening conditions such as HIV/AIDS and related opportunistic diseases. This paper explores some critical issues related to FTAs, examines some of the pressure impacting on the negotiations, reviews the trends around the protection of pharmaceutical patents in some recently concluded agreements, and considers their implications for SACU countries