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The Aetiology of Neonatal Infection in South Asia study is a major effort to determine the causes of community-acquired neonatal infections. It involves collecting epidemiological, clinical and laboratory data in 5 sites in 3 countries. The field and laboratory research operations are streamlined to maintain integrity and validity while operating in complex and variable environments. We developed a customized system for implementation of labeling and tracking biological specimen in both rural and urban community settings and integrated into all study laboratories. This report outlines the development and implementation of this harmonized system.The system links and tracks specimens with study participants and results generated from laboratory tests. Each biological specimen and its aliquots are tracked through key steps of the protocol, from collection and transport through molecular testing and long-term storage.The labeling and tracking system allows for standardization and monitoring of laboratory processes and improves the accuracy of Aetiology of Neonatal Infection in South Asia data. Community-based scientific projects could greatly benefit by adopting this, or a similar, system for specimen tracking and data linkage.