Drug disposition in children is impacted by developmental changes in drug absorption, distribution, metabolism and excretion. This mandates the need for dosing regimens specifically tailored to children. Yet, there are gaps in the knowledge on these developmental changes, for example regarding hepatic and renal drug transport and drug metabolism, putting children at risk for subtherapeutic or toxic drug exposure. Pediatric drug research is faced with ethical and analytical challenges. This review addresses how these knowledge gaps can be filled and challenges can be overcome by using innovative study designs.