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Low serum ferritin concentrations at birth, which reflect neonatal iron stores, track through to early childhood and have been associated with poorer neurodevelopmental outcomes. We aimed to identify maternal, antenatal and birth-associated factors that influence iron stores at birth in a prospective maternal-infant birth cohort.In a population-based, longitudinal, birth cohort in Ireland, 413 maternal-infant dyads with prospectively collected lifestyle and clinical data from 15 weeks' gestation had umbilical cord serum ferritin concentrations measured. Regression models were developed to identify independent factors associated with cord ferritin concentrations.Median (IQR) cord ferritin concentrations were 185.7 (131.7, 385.5) μg/l, and 8% (n = 33) of infants had low iron stores (ferritin < 76 μg/l) at birth. Maternal obesity (BMI ≥ 30 kg/m2) at 15 weeks' gestation (adj. estimate (95% confidence interval (CI)): -66.4 (-106.9, -25.9) μg/l, P < 0.0001) and delivery by caesarean section (-38.8 (-70.2, -7.4) μg/l, P = 0.016) were inversely associated with cord ferritin concentrations. In addition, maternal smoking at 15 weeks' gestation (adj. odds ratio (95% CI): 2.9 (1.2, 7), P = 0.020) and being born small-for-gestational age (3.4 (1.3, 8.9), P = 0.012) were associated with an increased risk of low iron stores (ferritin < 76 μg/l) at birth.We have identified a number of potentially modifiable lifestyle factors that influence iron stores at birth, with the important role of overall maternal health and lifestyle during pregnancy highlighted. Public health policies targeting women of child-bearing age to improve nutrition and health outcomes should be prioritised for the health of the next generation.