Little is known about the relationship between low birth weight (BW), as a marker of under-nutrition in utero, and childhood body mass index (BMI) and adiposity parameters, including skinfold thickness, abdominal subcutaneous (SAT) and visceral adipose tissues (VAT) and intramyocellular accumulation of lipids (IMCL). The EPOCH Study (Exploring Perinatal Outcomes among Children) explored the association between BW and markers of adiposity in contemporary, multi-ethnic children from Colorado. A total of 442 youth age 6–13 years (50% male, mean age 10.5 years) had anthropometric measurements, abdominal SAT and VAT measured by magnetic resonance imaging and IMCL deposition in the soleus muscle measured by nuclear magnetic resonance spectroscopy. BW and gestational age were ascertained from an electronic perinatal database. A weak positive association between BW and current BMI (P = 0.05) was seen, independent of demographic, perinatal, socio-economic and current lifestyle factors. When adjusted for current BMI, every one standard deviation decrease in BW (∼500 g), was associated with a 8.8 cm2 increase in SAT, independent of potential confounders. In conclusion, in a contemporary cohort of youth, BW was positively, but weakly, associated with BMI and inversely, though weakly, associated with SAT, independent of current BMI. There were no significant associations between BW and waist circumference, skinfolds, VAT and IMCL. Our results provide some support to the hypothesis that under-nutrition in utero, as reflected by lower BW, is associated with lower overall childhood body size, but an increased propensity for abdominal adiposity, reflected in this young age-group, predominantly as subcutaneous fat.