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Non-invasive screening tools to identify children at high risk of vitamin D (VitD) deficiency are proactive measures in preventive care. Recently, a validated questionnaire (Evaluation dEficieNCy Questionnaire, EVIDENCe-Q) for identifying newly diagnosed VitD-insufficient adults has been developed. We tested the EVIDENCe-Q modified for children with obesity and evaluated the correlation between VitD and questionnaire scores to adapt this tool to the pediatric population. We enrolled 120 children with obesity (BMI ≥ 2). Clinical evaluation and VitD levels were considered. The modified EVIDENCe-Q included information regarding factors affecting control of VitD, with scores ranging between 0 (best) and 36 (worst). VitD and adiposity indices were inversely correlated. The threshold values for identifying severe deficiency (<10 mg/dL), deficiency (<20 mg/dL) and insufficiency (<30 mg/dL) were scores of 21, 19 and 23, respectively. According to those thresholds, the prevalence of severe deficiency, deficiency and insufficiency was 47.5%, 69.2% and 23.3%, respectively; the best accuracy was obtained with a questionnaire score cut-off of 19 for the VitD deficiency level. A novel simple screening tool such as the modified EVIDENCe-Q would be useful in clinical practice to identify potential cases of hypovitaminosis D and select at-risk patients. Considering the limited accuracy and specificity of our results, for the pediatric population a dedicated tool should be created. Phases of childhood and the role of adipose tissue could be considered in the definition of a questionnaire intended for pediatric patients with obesity.