In the wake of the attacks of September 11, 2001, the United States of America embarked upon a major counter-terrorism campaign against al Qaeda and its affiliates. The conflict has involved ground combat operations in Afghanistan, as well as ancillary actions in Pakistan, Yemen and Somalia. In all of these theaters, the use of Unmanned Aerial Vehicles (UAVs) has increased dramatically; in recent years, armed UAVs have been used to conduct strikes in Yemen and Pakistan. The rapid growth of UAV operations shows no sign of slowing, and the implications of their use need to be continually examined if the United States wishes to achieve its policy objectives in Pakistan and Yemen. Comparing these cases will help bring together knowledge gained in studying each case separately. This thesis investigates how the use of UAVs as part of the counter-terrorism campaigns in Yemen and Pakistan has affected U.S. relations with those countries and whether the current arrangements are the best policies to combat terrorism in these countries.