The foreign direct investment (FDI) can be substitute for the contractual transfer of intellectual property rights in a situation where these rights are weakly protected. Hence, stronger intellectual property rights protection may reduce incentives for FDI. This is, however, only one line of reasoning. Stronger intellectual property protection can also increase motivation to invest into completely new products and processes. Thus, from the slightly different perspective FDI and strength of intellectual property protection can be seen as complementary. This duality of impact makes the search for efficient protection very difficult and complex. The aim of this paper is to outline the policy choices open for Estonia in influencing the relative strength of intellectual property rights protection and its impact on FDI. The vital secondary research agenda by this concerns the influence of EU-membership on the autonomy of such policy choices. Given the fact that there exist European patents and patent registry, certain intellectual property rights protection measures and legislative practices are undoubtedly pre-determined by this embeddedness into EU-wide protection systems. The national level policies and enforcement issues may still vary.