The practice of evidence-based medicine is based on the results of properly designed, conducted and analyzed studies. Evidence for the safety and efficacy of therapies is established through clinical trials. However, there are a number of difficulties in the design and management of clinical trials in children. We explore the theoretical and ethical issues and difficulties of designing and conducting clinical trials in children, and illustrate the ways in which these challenges were encountered in two clinical trials assessing anticoagulant therapy in children with thrombophilia (PROTEKT (PROphylaxis of ThromboEmbolism in Kids Trial) and REVIVE (REVIparin in Venous ThromboEmbolism)). Means for overcoming these challenges are also addressed.