Background : International Health Regulations require countries to establish laboratory systems for rapid and safe confirmation of public health emergencies.Objective : This study assessed the capacity of the National Laboratory System for the detection of infectious threats to global health security in Benin.Method : The study was descriptive, cross-sectional, and evaluative. The targets were laboratories performing the confirmation of infectious threats. The sampling method was non-probabilistic with the reasoned choice of 74 laboratories. Four collection tools were used. The World Health Organization’s laboratory assessment tool for health facilities was used to assess the national public health laboratory. The assessment was based on the capacities of peripheric laboratories and of the national reference laboratory. The capacity was rated good if at least 80% of peripheric laboratories met at least 80% of the criteria and if the national public health laboratory had an average indicator of at least 80%. Otherwise, the capacity was rated insufficient.Results : The national laboratory system capacity was insufficient. Only 54% of peripheric laboratories had good capacity. The national reference laboratory had an average indicator of 71%. In this reference laboratory, specimen collection and transport, laboratory testing performance, consumables and reagents, and public health functions had the best scores, above 80%. Biorisk management, organization and management, and documents had the lowest scores. In peripheric laboratories, the testing performance was the only domain with good capacity.Conclusion : To ensure effective Global Health Security in Benin, a National Laboratory System capacity improvement strategic plan need to be developed and implemented.