Even though the regulatory authorities to some extent accept the extrapolation of efficacy data from adults to paediatric patients, it is often the case that differences in the disease process and the developmental stage of the children prevent the extrapolation of efficacy in these populations. Where efficacy studies are needed, the development, validation, and employment of different endpoints for specific age and developmental subgroups become necessary. Children are in continuous development and any measure to assess the efficacy of an intervention should take carefully into account how this development affects the endpoints, including the performance capacity of the child and differences in the condition and symptoms presented. Clinical endpoints that are used in the adult trials to evaluate treatment effect may not be suitable in paediatric studies. The development of surrogate endpoints for benefit and risk assessment in children is necessary. Collaboration between the academic researchers, pharmaceutical industry, and regulatory authorities is needed to meet the challenges in proper validation of biomarkers and surrogate endpoints in paediatric trials.