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The US-led ‘war on terror’ dramatically changed America’s security strategy towards Africa. But more fundamentally, it threw the Horn of Africa on the centre stage of global counter-terrorism. A double-edged blade, counter-terrorism has at once catalysed peace processes and intensifi ed insecurity, with Islamic radicalism at the core of the regional storm. Governments utilised the threat of terrorism for political ends, defending old security paradigms that prioritised regime stability over human security. Africa integrated counter-terrorism into its emerging security agenda, but insuffi cient funds, operational constraints and poor coordination with international initiatives have hampered meaningful progress. Washington, laudably, launched a robust counter-terrorist campaign, but its high-handed military-heavy style put fragile democracies at risk while lapses in its overall policy risk triggering proxy wars. This essay examines the impact of counter-terrorism on security in the Horn of Africa. It argues for stronger coordination between national, regional and international initiatives to curb international terrorism.