Security and intelligence are alternative approaches to counter-terrorism policies. Which one of them is more appropriate for Balkan counter-terrorism policies? I argue that the selection of a policy strategy should depend on the risk assessment of the overall Balkan conflict potential. This article aims to show that a major threat to the Balkan politics and state are currently local ethno-national conflicts. The latter – although considerably contained – still destabilise the Balkan region by sporadic campaigns of local terrorism and provide incentives for local terrorist groups to seek co-operation with global terrorism and trans-state crime syndicates. Drawing on regional risk assessment, I argue that security studies and intelligence should inform and complement each other in the planning of counter-terrorism strategies in the Balkans. However, security studies should take the lead and counter-terrorism strategies should be discussed in the context of conventional peace-keeping aimed at the rehabilitation of post-conflict societies and states.