Iron deficiency is the most common micronutrient deficiency worldwide. Iron is essential for the development of multiple organ systems, most especially the developing brain. Iron deficiency, particularly during sensitive periods of brain development, such as in early childhood, is associated with long-lasting adverse consequences for cognition, motor function and behaviour. Little consideration has been given to iron deficiency in newborn infants and its potential health consequences. Fetal iron accretion is compromised by pregnancy complications such as pre-term birth and gestational diabetes mellitus, and our work has identified an increased risk of low iron stores at birth from maternal lifestyle factors such as smoking and obesity. Early-life events, including Caesarean section delivery, further add to the cumulative risk of neonatal iron deficiency, which can persist throughout infancy into early childhood. While investigations into the long-term neurological consequences of neonatal iron deficiency are limited, there is evidence of poorer memory, motor function and language ability in children born iron deficient. Recently, we also identified significant behavioural consequences of neonatal deficiency persisting from 2 to 5 years of age, with effects particularly apparent in ‘high-risk’ children born to obese or smoking mothers or delivered by Caesarean section. Interventions targeting the fetal/neonatal period could therefore represent a key opportunity for the prevention of iron deficiency and its associated long-term health consequences. A dual approach is required, comprising public health strategies targeting prevention, to improve health in women of reproductive age, and the development of screening strategies for the early detection of iron deficiency in newborn infants.