Mortality rates in neonatal surgery have dropped markedly, illustrating the enormous progress made. Yet, new questions have arisen. To mention one, health care budgets have tightened. It follows that the effects of medical interventions should be weighted against their costs. As evidence was particularly sparse, we set out to analyse cost-effectiveness of neonatal surgery. The purpose of this article is to summarise our findings and to review recent studies. Moreover, this article explains the relevance of cost-effectiveness analysis and explores how cost-effectiveness interacts with other determinants of health care priority setting. Our research revealed that treatments for two common diagnostic categories in neonatal surgery (congenital anorectal malformations and congenital diaphragmatic hernia) produce good cost-effectiveness. Other groups also published cost-effectiveness studies in the field of neonatal surgery, although their number is still small. Contemporaneously, the economic aspects of health care have captured the interest of policy makers. Importantly, this is not to say that there are no other factors playing a role in priority setting, foremost among which are ethical questions and arguments of equity. This article concludes that, according to present evidence, neonatal surgery yields good value for money and contributes to equity in health.