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The issue of balancing free trade with the protection of values, national regulatory autonomy and sovereignty has recently been accentuated in the area of fundamental (human) rights. It is well established case law that fundamental rights are a part of the general principles of Community law protected by the Court, but their precise status in the EU legal order has remained unclear up to the present. Particularly questionable is the issue of the hierarchy of these rights in relation to Treaty provisions. This paper focuses on the interaction between fundamental rights and fundamental (market) freedoms, and it analyses the implications of the case law dealing, on the one hand, with their mutual enhancement and, on the other hand, with their potential conflicts. Both types of cases raise sensitive constitutional issues, because, while supporting fundamental rights protection, there is an occasional lack of concern for other interests that national regulators seek to protect.