Surveillance of fetal alcohol syndrome (FAS) is important for monitoring the effects of prenatal alcohol exposure and describing the public health burden of this preventable disorder. Building on the infrastructure of the Fetal Alcohol Syndrome Surveillance Network (FASSNet, 1997-2002), in 2009 the Centers for Disease Control and Prevention awarded five-year cooperative agreements to three states, Arizona, Colorado, and New York, to conduct population-based surveillance of FAS. The Fetal Alcohol Syndrome Surveillance Network II (FASSNetII, 2009-2014) developed a surveillance case definition based on three clinical criteria: characteristic facial features, central nervous system abnormalities, and growth deficiency. FASSNetII modified the FASSNet methods in three important ways: 1) estimation of a period prevalence rather than birth prevalence; 2) surveillance of FAS among school-age children (ages 7-9 years) to better document the central nervous system abnormalities that are not apparent at birth or during infancy; and 3) implementation of an expert clinical review of abstracted data for probable and confirmed cases classified through a computerized algorithm. FASSNetII abstracted data from multiple sources including birth records, medical records from child development centers or other specialty clinics, and administrative databases such as hospital discharge and Medicaid. One challenge of FASSNetII was its limited access to non-medical records. Therefore, the FAS prevalence that could be estimated was that of the population identified through an encounter with the healthcare system. Clinical and public health programs that identify children affected by FAS provide critical information for targeting preventive, medical and educational services in this vulnerable population.