Background It is known that height and body mass index (BMI) are correlated in childhood. However, its impact on the (trend of) national prevalence rates of overweight and obesity has never been investigated. The aim of our study is to investigate the relation between height and national prevalence rates of overweight and obesity in childhood between 1980, 1997, and 2009, and to calculate which fixed value of p (2.0,2.1, …,3.0) in kg/mp during childhood is most accurate in predicting adult overweight. Methods and findings Cross-sectional growth data of children from three Dutch nationwide surveys in 1980, 1997, and 2009, and longitudinal data from the Terneuzen Birth Cohort and the Harpenden Growth Study were used. Relative risks (RR) and 95% confidence intervals (CI) were calculated. Our study showed that tall (>1 standard deviation (SD)) girls aged 5.0–13.9 y were more often overweight (RR = 3.5,95%CI:2.8–4.4) and obese (RR = 3.9,95%CI:2.1–7.4) than short girls (<−1 SD). Similar results were found in boys aged 5.0–14.9 y (RR = 4.4,95%CI:3.4–5.7 and RR = 5.3,95%CI:2.6–11.0). No large differences were found in the other age groups and in comparison with children with an average stature. Tall boys aged 2.0–4.9 y had a significantly higher positive trend in overweight between 1980 and 1997 compared to short boys (RR = 4.0,95%CI:1.38–11.9). For other age groups and in girls, no significant trends were found. The optimal Area Under the Curve (AUC) to predict adult overweight was found for p = 2.0. Conclusions and significance Tall girls aged 5.0–13.9y and tall boys aged 5.0–14.9y have much higher prevalence rates of overweight and obesity than their shorter peers. We suggest taking into account the impact of height when evaluating trends and variations of BMI distributions in childhood, and to use BMI to predict adult overweight.