The article analyzes three different cases of clinical research in which children are asked to participate. Participation of children in researches is one of the major challenges for Bioethics and societies nowadays due to the tensions and issues concerning the guarantee of rights in clinical research, the responsibilities of the different actors involved, and the purpose of improving the quality of life without affecting scientific freedom and new knowledge production. The aim of the article is to establish the way in which autonomy is exercised, considering ethical and regulative aspects within clinical research involving children. In order to achieve such a purpose, case study research methodology is employed, revealing the tensions and ethical issues involved in this particular kind of clinical research as well as considering international documents and the national regulation regarding this particular problem.