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Background: The monitoring of head circumference (HC) is essential to early detect any conditions affecting its growth in early childhood. A positive secular trend and regional specificities in HC suggested the need to provide updated national HC reference growth charts. Methods: We extracted all growth data collected from 42 primary-care physicians from across the French metropolitan territory who used the same electronic medical-records software. We selected HC measurements up to age five years for all children who were born after 1990 with birth weight > 2500 g. We derived new HC growth charts by using Generalized Additive Models for Location, Scale and Shape, then externally validated them until 30 months of age by comparison with the national population-based Étude Longitudinale Française depuis l'Enfance (ELFE) birth cohort and compared them to previous French and WHO growth charts. Findings: With 973,869 HC measurements from 157,762 children, new calibrated HC growth charts from birth to age five years were generated. The new HC growth charts showed good external fit by comparison with the ELFE birth cohort. As compared with the new HC growth charts, the previous French and WHO growth charts mean HC z-scores were, respectively, -0.4 and -0.6 SD for girls and -0.2 and -0.6 SD for boys. Interpretation: We produced and validated national calibrated HC growth charts by using a novel big-data approach applied to data routinely collected in clinical practice. Comparison with previous French and WHO growth charts confirmed a positive secular trend since the 1960s and regional specificities. Funding: The French Ministry of Health; Laboratoires Guigoz—General Pediatrics section of the French Society of Pediatrics—Paediatric Epidemiological Research Group; the French Association of Ambulatory Pediatrics; and educational grant from the Regional Health Agency of Ile-de-France.