Ongoing advancements in the pre- and postoperative care of the neonate with a surgical condition have enabled the survival of an increasing number of infants with congenital malformations. For decades, surgeons have insisted on a regular self-examination of outcomes to ensure the optimal treatment of our patients. Outcome analysis traditionally relates to the rudimentary end result of an operation—utilizing variables such as mortality, operative time, specific complication rates (i.e., incidence of esophageal stricture following esophageal atresia [EA] repair), and hospital length of stay, to name a few. Recently, outcomes research has become a more complex endeavor. Measures of long-term outcomes, including “functional outcome” and “health-related quality of life,” are equally important to the morbidity sustained as a result of a congenital malformation and its attendant surgical correction. The methods by which subjective assessments are expressed as a quantitative measure are therefore important for the newborn surgeon to understand. These data serve as an important adjunct to prenatal counseling, offer information about future health expectations for families, assist the surgeon in identifying potential improvements in perioperative management, and will likely be utilized by public agencies charged with implementing health policy, especially in an era of diminishing resources. Therefore, long-term outcomes are of specific import to the neonates we care for, the families we answer to, and our colleagues charged with the continued efforts to improve the surgical care of our youngest patients. This chapter will begin by focusing on the specific language and methodology of modern long-term outcomes research as a prelude to the current status of long-term outcomes assessment in newborn surgical conditions commonly treated by the pediatric surgeon.