The paper examines constitutional courts' responses to systemic or real risks encroaching upon judicial independence and other risks undermining the rule of law in the Member States. It will examine the CJEU's case law dealing with the principle of mutual trust between the Member States, particularly with regard to the area of freedom, security and justice, and the reactions from the national level (e.g. case law of constitutional courts). Should constitutionally protected rights always yield before the uniformity, effectiveness and primacy of EU law, under the principle of mutual trust, as the case of Melloni might be understood? Under what circumstances will the CJEU defer to the national level of protection and how do constitutional courts respond to the CJEU's case law? What are the ensuing implications for horizontal and vertical judicial cooperation based on mutual recognition?