Abdominal adiposity and metabolic ill health in Asian Indians are a growing public health concern. Causal pathways are unknown. Preventive measures in adults have had limited success. The aim of this observational case-control study was to compare adipose tissue partitioning in 69 healthy full term Asian Indian and white European newborns born in Pune, India and London, UK, respectively. The main outcome measures were total and regional adipose tissue content measured by whole body magnetic resonance imaging. Although smaller in weight (95% CI for difference −0.757 to −0.385 kg, p < 0.001), head circumference (−2.15 to −0.9 cm, p < 0.001), and length (−2.9 to −1.1 cm p < 0.001), the Asian Indian neonates had significantly greater absolute adiposity in all three abdominal compartments, internal (visceral) (0.012–0.023 L, p < 0.001), deep s.c. (0.003–0.017 L, p = 0.006) and superficial s.c. (0.006–0.043 L, p = 0.011) and a significant reduction in nonabdominal superficial s.c. adipose tissue (−0.184 to −0.029 L, p = 0.008) in comparison to the white European babies despite similar whole body adipose tissue content (−0.175 to 0.034 L, p = 0.2). We conclude that differences in adipose tissue partitioning exist at birth. Investigative, screening, and preventive measures must involve maternal health, intrauterine life, and infancy.