BACKGROUND: While health technology assessment (HTA) increasingly informs allocative decision-making, the extent to which HTA can be applied to children demands scrutiny. Pediatric economic evaluation is complicated by dependency on parents, specific disease characteristics, and dynamic states of cognitive, emotional, and physical development. Chronic disease is rare in children, leading to difficulties in conducting trials and establishing evidence. Since disabilities that start in childhood may be carried into adulthood, it is also important to measure long-term costs and consequences. Long-term data may not be available or may be uncertain. Furthermore, assessments in children must consider externalities including parent productivity losses, family quality of life decrements, impacts on school performance and education, and effects on future employment. Pediatric HTA must also take into account impacts on non-health sectors, including education and social services. OBJECTIVES: To understand the evidence gap in child HTA.  METHODS: The Centre for Reviews and Dissemination database was searched for pediatric reports published from 2003-2008. Of 147 reports, 84% came from Europe or North America. The most common intervention category was screening programs (18%), such as for conditions related to hearing, vision, or speech impairment, cystic fibrosis, hematologic-metabolic syndromes, overweight, and psychosocial problems. A comparison between adult and pediatric HTAs was undertaken for 222 reports published in 2007-2008. RESULTS: Whereas the most common conditions studied in adults were cancer, cardiovascular disorders and rheumatological disorders, diseases most commonly studied in children were asthma, autism, cystic fibrosis and diabetes. In addition to differences between adults and children related to measurement, analysis and the availability of evidence, the social, legal and ethical issues that influence decision-making are unique for children due to their vulnerability and lack of autonomy. CONCLUSIONS: As HTA increasingly becomes the basis for decision-making, the challenges in applying HTA to child health must be considered to ensure equity in health care policy.