Epidemiological and animal studies have suggested an effect of the intrauterine milieu upon the development of childhood obesity. This study investigates the relationship between body composition measured by dual energy X-ray absorptiometry expressed as body fat percent, body fat mass index (BFMI), and fat free mass index (FFMI) in obese children and the preceding in utero conditions expressed by birth weight, birth length, and birth weight for gestational age. The study cohort consisted of 776 obese Danish children (median age 11.6 years, range 3.6–17.9) with a mean Body Mass Index Standard Deviation Score (BMI SDS) of 2.86 (range 1.64–5.48) treated in our national referral centre. In a linear general regression model adjusted for age, gender, socioeconomic status, and duration of breastfeeding, we found the body fat percent, FFMI, and BFMI at the time of enrolment in childhood obesity treatment to be significantly correlated with both birth weight and birth weight for gestational age. Conclusion: These results indicate a prenatal influence upon childhood obesity. Although there are currently no sufficient data to suggest any recommendations to pregnant women, it is possible that the prenatal period may be considered as a potential window of opportunity for prevention of childhood overweight and obesity.