For newborn infants in intensive care units, the morbidity and mortality from infection continues to be a major burden despite advances in neonatal care. Infants are at risk for early-onset, late-onset as well as hospital-acquired infections. Research studies are needed to optimize timely diagnosis and treatment, and develop patient-specific and system-wide strategies to prevent perinatal and neonatal infections. To address the knowledge gaps that preclude optimal, evidence-based care in this critical field, the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) organized a workshop in August 2008. In this paper, we provide a summary of the discussions, focusing on major knowledge gaps, and prioritized suggestions for research in this area.