This paper examines the increasing importance of EU external cooperation in the field of criminal justice and counter-terrorism and its impact on the interplay between justice and home affairs and common foreign and security policy. It goes on to look at the effect of counter-terrorism policy on the listing of terrorist organisations, and the effect that moves to combat the financing of terrorism in this field has on NGOs. It studies the ways in which such cooperation can be used to promote human rights. Finally, it highlights the problem of accountability for human rights abuses in international cooperation on counter-terrorism and in rule of law missions, particularly as the EU is not a signatory to the ECHR and the EU Charter is not yet binding. All of these issues are addressed broadly and with a specific focus on EU-Canada cooperation.