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This paper examines two case studies of how the United States-led ‘Global War on Terror’ has impinged on the Philippine government’s peace negotiations with the country’s two major rebel groups: the Moro Islamic Liberation Front (MILF) and the communist-led National Democratic Front (NDF). For four decades, these homegrown rebellions, not externally inspired terrorism, have been the main national or human security problem of the Philippines. The Global War on Terror has caused significant damage to the Philippine peace process aiming to end these conflicts. This contradicts the view that the Global War on Terror has boosted these processes by keeping these rebel groups honest through ‘terrorist organisation’ designations and listings, as well as the very definition of terrorism as applied to these groups. These designations should not be loosely applied on the basis of isolated terrorist acts; such acts must be systematically employed by the concerned organisation to characterise it as a terrorist organisation.