Bibliometric impact analyses show that Swedish research has less international visibility than Danish research. When taking a global view on all subject fields and selecting publications cited higher than the 90th percentile, i.e., the Top 10 %—publications, the Swedish Research Council shows that although Sweden ranks 15 % above world average, Denmark, the Netherlands and Switzerland rank 35-40 % above. To explain these different performances, The Royal Swedish Academy of Sciences asked us to compare the national research systems on three levels: priority setting at national level, governance of universities and direction and funding of research. There are of course many similarities between the Danish and Swedish research systems but there are still subtle differences that have developed over time, which may explain the different international visibility. First of all, it does not depend on different levels of public spending on research and development. However, the core funding of universities relative external funding is higher in Denmark than in Sweden. The academic leadership of Danish universities in terms of board, vice-chancellor, faculty dean and department chair is also more coherent and focused on priority setting, recruitment, organization and deployment of resources to establish research environments that operate at the forefront of international research. On all these points we see a weaker leadership in Sweden. Furthermore, over the last 20 years, public funding of research in Sweden has become more and more unpredictable and program oriented with many new actors, while the Danish funding system, although it also has developed over time, shows more consistency with strong actors to fund individuals with novel ideas. The research policy in Sweden has also developed multiple, sometimes even conflicting goals, which have undermined conditions for high-impact research, while in Denmark a policy to support excellence in research has been more coherent.