Legal protection for pharmaceutical innovations in the EU involves patents, supplementary protection certificates (SPC) and data exclusivity. The particular rights serve substantially the same purposes and overlap both in subject matter and in time, which raises doubts about their justification. This complex system has been built through various initiatives, including international agreements, legal acts at the Community level and national laws. The legal structure has been shaped extensively by case law, especially judgments of the Court of Justice of the European Union and decisions of the European Patent Office. This chapter presents how the particular legal instruments evolved and how they have influenced the scope of protection for pharmaceuticals. An overview of the legislative and case law milestones, as well as analysis of their rationales, allows for a better understanding of how the balance of interests among many stakeholders has been sought.