Current knowledge on obesogenic effects of persistent organic pollutants (POPs) is equivocal. We therefore evaluated the associations between early-life POP exposures and body mass index (BMI) in 444 Faroese children born in 2007–2009. POPs were measured in maternal 2-week postpartum serum and child age-5 serum. Linear regression and generalised linear models assessed the associations with continuous and dichotomous BMI z-scores, respectively, at ages 18 months and/or 5 years. Maternal serum concentrations of HCB, PFOS and PFOA were associated with increased BMI z-scores and/or overweight risk (i.e. BMI z-score≥ 85th WHO percentile). No clear association was found for maternal serum-PCBs, p,p’-DDE, PFHxS, PFNA and PFDA. In cross-sectional analyses, we observed a pattern of inverse associations between child serum-POPs and BMI z-scores at age 5, perhaps due to reverse causation that requires attention in future prospective analyses. Findings in this recent cohort support a role of maternal exposure to endocrine disruptors in the childhood obesity epidemic.