The study focuses on the implementation of inquiry-based science education (IBSE) within the 7FP ESTABLISH project and its impact on pupils. The project included the creation of education units and realization of courses for teachers with the goal of educating teachers on IBSE. This was then followed by the implementation of IBSE education units into the teaching schedule of teachers who completed the respective courses. The impact of IBSE on pupils was evaluated using adopted and adjusted evaluation tools. The evaluation focused on the impacts on pupils’ intrinsic motivation for learning natural sciences, understanding the importance of natural sciences for society and pupils’ epis- temological beliefs. The study discusses the results obtained in Slovakia and focuses especially on gender differences.