Regional differences in adipose tissue distribution are associated with differences in adipocyte metabolism and obesity-related morbidities. Intrauterine growth restriction appears to place individuals at greater risk of obesity associated morbidities in later life. Despite this, little is known regarding the quantity and distribution of adipose tissue in infants during early development. The aim of this study was to compare total and regional adipose tissue content in appropriate-for-gestational-age (AGA) and growth-restricted (GR) newborn infants born at or near term. Whole body adipose tissue magnetic resonance imaging (MRI) was performed as soon as possible after birth. Total and regional adipose tissue depots were quantified. A total of 35 infants (10 GR; 25 AGA) were studied. Mean (SD) total percentage adipose tissue was lower in GR infants than AGA infants [GR: 17.70% (2.17); AGA: 23.40% (3.85); p = 0.003]. This difference arose from differences in subcutaneous adipose tissue mass [mean (SD) percentage subcutaneous adipose tissue mass, GR: 16.13% (2.20); AGA: 21.44% (3.81); p = 0.004], but not intra-abdominal adipose tissue mass [mean (SD) percentage intra-abdominal adipose tissue, GR: 0.42% (0.22); AGA: 0.61% (0.31); p = 0.45]. In contrast to subcutaneous adipose tissue, intra-abdominal adipose tissue is not reduced in infants with intrauterine growth restriction. This suggests that subcutaneous and intra-abdominal adipose tissue compartments may be under different regulatory control during intrauterine life.