The relations between the two international organizations, namely the EU and the UN, have been characterized in general as harmonized and cooperative. In this research however, we are more interested to examine cases where the EU has not been characterized as much “cooperative” and has chosen a different path than the UN. In particular this research contributes in the relations between the EU and the UN in imposing sanctions. It has been noticed that in most cases the EU implements the UN sanctions and follows the same logic, but it had been noticed as well cases when the EU unilaterally or multilaterally has imposed sanctions against a state without having supported its decision on UN resolutions and even cases when the EU showed a tendency not to implement UN sanctions, since it noticed that the sanctions are not in a light with fundamental human rights guaranteed by the European Convention for Human Rights. This study highlights the legal and political issues arising from the efforts of the implementation by the EU of the UNSCRs and more specifically Resolutions related to suspects of terrorism.