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Introduction: Exposure to endocrine disruptors during early childhood poses significant health risks. This study examines the exposure levels of French 3.5-year-old children to various persistent and non-persistent pollutants and pesticides using hair analysis as part of the ELFE national birth cohort. Differences in sex and geographical location among the children were investigated as ppossible determinants of exposure. Methods: Exposure biomarkers from 32 chemical families were analyzed using LC-MS/MS and GC-MS/MS in 222 hair samples from children in the ELFE cohort. Of these, 46 mother–child pairs from the same cohort provided unique insight into prenatal and postnatal exposure. Regressions, correlations and discriminate analysis were used to assess relationships between exposure and possible confounding factors. Results and Discussion: Among the biomarkers tested in children’s hair samples, 69 had a detection frequency of ≥ 50 %, with 20 showing a 100 % detection rate. The most detected biomarkers belonged to the bisphenol, organochlorine and organophosphate families. Sex-specific differences were observed for 26 biomarkers, indicating the role of the child’s sex in exposure levels. Additionally, regional differences were noted, with Hexachlorobenzene varying significantly across the different French regions. Nicotine presented both the highest concentration (16 303 pg/mg) and highest median concentration (81 pg/mg) measured in the children’s hair. Statistically significant correlations between the levels of biomarkers found in the hair samples of the mothers and their respective children were observed for fipronil (correlation coefficient = 0.32, p = 0.03), fipronil sulfone (correlation coefficient = 0.34, p = 0.02) and azoxystrobin (correlation coefficient = 0.29, p = 0.05). Conclusions: The study highlights the elevated exposure levels of young children to various pollutants, highlighting the influence of sex and geography. Hair analysis emerges as a crucial tool for monitoring endocrine disruptors, offering insights into exposure risks and reinforcing the need for protective measures against these harmful substances.