Genetic, physiological, parental and behavioral factors influence body weight status in a Dutch children cohort at the age of 13 years. Additionally, the role of puberty is important at ages 12 and 13 years, so it is of interest to determine the development of these variables from 12 to 13 years. The aim of the study was to identify the role of genetic, physiological, parental and behavioral factors in the development of body-weight (BW). In a Dutch cohort of 94 children, anthropometric measurements were determined from birth until 13 years. At 7, 12 and 13 years, also body composition, leptin concentrations, TFEQ scores and physical activity were determined; 3 genetic polymorphisms were determined as well. The results showed that the overweight boys and girls (11%) had higher BW, waist circumference, body fat percentage, fat mass, leptin concentrations, factor 1 and 2 TFEQ scores. Leptin concentrations at 7 years, BW gain during 0–1 years and body mass index (BMI) at 4 years were related to genetic polymorphisms. A peak in leptin concentrations between age 7 to 13 years was shown at 12 years. In lean boys, the decrease between 12 and 13 years was related to an increase in fat free mass. Overweight children's parents had a higher BW, BMI, factor 1 and 2 TFEQ scores, compared to lean children's parents. In conclusion, in addition to the effects of genetic, parental and behavioral factors in the development of body-weight in children from a longitudinal point of view, leptin appeared to play an important role in the development of body composition during puberty.