Background: Body composition in early life influences the development of obesity during childhood and beyond. It is, therefore, important to adequately determine neonatal body composition. Fetal growth and maternal factors might influence neonatal fat mass percentage (FM%), independent of birth weight. Methods: In 194 healthy neonates, we investigated neonatal body composition, measured by air-displacement plethysmography (PEAPOD), and its associations with estimated fetal weight (EFW), neonatal anthropometric data, maternal preconceptional body mass index (BMI) and maternal weight gain during pregnancy. Results: There was a large variation in neonatal FM%, even in case of a similar birth weight, corrected for gender and gestational age. Neonatal FM% was associated with EFW at 30 and 36 weeks of gestation and with catch-up in weight between 30 and 36 weeks of gestation, but not with EFW at 20 weeks (p < 0.01, p < 0.01 and p = 0.64, respectively). Neonatal FM% was also associated with preconceptional BMI of the mother (p < 0.01). There was no correlation with maternal weight gain. Conclusion: Our study shows that term neonates have a large variation in FM%. Neonatal FM% is associated with EFW at 30 and 36 weeks, catch-up in weight between 30 and 36 weeks of gestation and preconceptional BMI of the mother.