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Purpose: We determined the association of total sugar intake with body weight and fat mass in children on an energy-equivalent basis and potential changes in the association from 2 to 8 years of age. Methods: Data were available from the Childhood Obesity Project Trial initiated in 2002. Sugar intake was measured by 3-day weighed food protocols at 2, 3, 4, 5, 6, and 8 years of age. Body mass index (BMI) and fat mass index (FMI) were available at the same time points. To investigate the association of sugar intake with anthropometrics over time, linear mixed models were applied. Odds ratios for having a high BMI or FMI (above one standard deviation) were estimated by logistic random-effects models. To control for total energy intake, the residual method was chosen and models were additionally adjusted for total energy intake. Results: Data were available for 809 children with in total 2846 observations. In an isocaloric model, an increase of 100 kcal from sugar per day was significantly associated with lower zBMI (− 0.033; 95% CI −0.061, − 0.005) and zFMI (− 0.050; 95% CI − 0.089, − 0.011). In addition, a 100 kcal higher sugar intake was related to lower odds of having a high zBMI (OR 0.743; 95% CI 0.611, 0.903). Conclusion: This study provides no indication that increased total sugar intake positively affects BMI on an energy-equivalent basis. Whether the negative association of sugar is due to physiological effects or points more to macronutrient preferences or a reporting bias (lower sugar intake) in children with higher BMI can be debated. Clinical trial registry: ClinicalTrials.gov Identifier: NCT00338689; Registered: June 19, 2006. URL: http://clinicaltrials.gov/ct2/show/NCT00338689?term=NCT00338689&rank=1. [ABSTRACT FROM AUTHOR]