This thesis serves two aims. The first aim is to present the transatlantic divergences on human rights in counter-terrorism and reach below the surface to find out the underlying causes that account for the divergences. The exploration facilitates the discussion on the balance between counter-terrorism and Human Rights protection, which is the second aim of this thesis. Are we fighting against terrorism at the expense of human rights? If so, what are the remedies? The reasoning of the thesis is based on two hypotheses. First, the reason for the divergences of US and EU on human rights in the Anti-terror war mainly lies in their different strategic cultures as well as their past experiences with terrorism. Second, despite the fact that EU put more weight on human rights than US in the battle, counter-terrorism borders on becoming terror against terror at the expense of human rights. The purpose of counter-terrorism is questioned. A reconciliation between counter-terrorism and human rights protection is needed so that the purpose of counter-terrorism can be justified. As for the methodology of reasoning, for the first hypothesis I will start from how differently US and EU conceive the problem after 9/11 attacks, which illustrates the gulf in the strategic culture between the two sides of Atlantic. Due to the long experience with domestic menace , EU tend to put weight on multilateralism and the legal changes related to human rights are less sweeping than in US. The US, with no such experience like EU, acted unilaterally and started a global war with determination to eliminate terrorism at all costs. It follows that security concern is put high above human rights protection. Then concrete examples will be discussed to show the divergences on human rights protection in the war on terror as a result of different perceptions of the threat between EU and US. For the second hypothesis, facts of human rights violation in the war on terror will be presented. Also, critical analysis will be given to how ordinary people's private lives are interfered and how doubts about counter-terrorism arise. It leads to the recognition that counter-terrorism can only be justified when it is conducted under the principle of human rights protection.