Clinical trials (CTs) in children involve much methodological specificity that are reflected in the ethical issues related to them, as well as in the evaluation of ethical acceptability of the given protocol by an ethics committee. A child in comparison to an adult exhibits numerous patho/physiological differences that are in addition characterized by the quick changes during the child's growth and development. Nowadays, there are no doubts about the necessity of conducting specific CTs in children that are not possible to perform in adults. Despite children are not able to give legally valid informed consent and it is necessary to obtain consent from the child's parents, or from the legal representative, it is also necessary, before including the child into the trial, to obtain his/her appropriate agreement (assent) with participation. It is a must always to fully respect the requirements of minimization of pain, discomfort, fear, and separation from the parents especially from the mother. Special ethical issues are connected with CTs conducted in neonatal period. On the part of the professional public, producers of medicinal drugs, as well as from the positions of the European institutions, considerable attention is being paid to the area of CTs in children. It is reflected in numerous scientific researches, and professional and legislative activities. In the Slovak Republic, the area of biomedical research, including CTs, in children and minors is covered by up-to-date, comprehensive legislation. It ensures not only the maximal protection of the child or minor taking part in biomedical research or CT, but it also provides sufficient level of legal certainty to the sponsors and investigators of biomedical research projects/CTs.