Background: Glucose-6-phosphate dehydrogenase (G6PD) deficiency is one of the most common and widespread erythrocyte enzymopathy in the world. The aim of this study was to determine the prevalence and the factors associated with G6PD deficiency in infants and children in Parakou in 2014. Methods: The current cross-sectional descriptive study with analytical purpose was carried out from March to August, 2014 in the town of Parakou (Republic of Benin). Its target consisted of 510 infants and children aged between 1 to 60 months. They were selected by two - stages cluster random sampling. Results: The recorded prevalence of G6PD deficiency was 26.1% [CI95%: 22.4%-30.2%] and factors that were associated with that deficiency were health history of neonatal jaundice and fever (p=0.0137 and 0.0001 respectively). No relationship was established between G6PD deficiency and factors such as sex, ethnic group, consanguinity, previous hemolytic crisis, jaundice outside of neonatal period, and anemia. Among clinical signs, only fever and mucocutaneous pallor were significantly associated with the studied G6PD deficiency (p = 0.0001). Conclusion: Prevalence of G6PD deficiency is considerably high in Parakou. Therefore, the introduction of systematic neonatal screening is required.