The Emerging Infections Programs (EIPs), a population-based network involving 10 state health departments and the Centers for Disease Control and Prevention, complement and support local, regional, and national surveillance and research efforts. EIPs depend on collaboration between public health agencies and clinical and academic institutions to perform active, population-based surveillance for infectious diseases; conduct applied epidemiologic and laboratory research; implement and evaluate pilot prevention and intervention projects; and provide capacity for flexible public health response. Recent EIP work has included monitoring the impact of a new conjugate vaccine on the epidemiology of invasive pneumococcal disease, providing the evidence base used to derive new recommendations to prevent neonatal group B streptococcal disease, measuring the impact of foodborne diseases in the United States, and developing a systematic, integrated laboratory and epidemiologic method for syndrome-based surveillance.