Purpose: To inform current policy debate regarding the public health role in long-term follow-up for individuals with disorders identified through state newborn testing efforts, by identifying and assessing key challenges, quality assurance activities, and long-term follow-up perceptions of state newborn screening programs. Methods: A 23-question, web-based survey sent to newborn screening programs in all 50 states and Washington, DC, during January and February, 2005. Results: Many U.S. newborn screening programs do not currently engage in structured long-term follow-up for newborns with diagnosed disorders. The newborn screening programs that do long-term follow-up face various challenges that may impact their ability to perform it effectively. Barriers include a lack of comprehensive quality assurance practices, outsourcing, financial constraints, and perceived communication problems with providers who treat these patients. Conclusions: A more in-depth analysis of the desired and feasible roles that should be played by newborn screening programs in long-term follow-up is needed. The wide variability within programs regarding the structure and implementation of long-term follow-up, and the relative absence of long-term follow-up systems components in some newborn screening programs, poses an interesting question regarding responsibility for evaluation of longer-term outcomes associated with newborn testing and disorder diagnosis.