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BACKGROUND Fracture risk assessment in children with benign bone lesions of long bones remains poorly investigated. AIM To investigate the risk factors for pathological fracture in children with benign bone lesions and to propose a modified scoring system for quantitative analysis of the pathologic fracture risk. METHODS We retrospectively reviewed 96 pediatric patients with benign bone lesions. We compared radiographic and clinical features between 40 patients who had fractures through a benign bone lesion and 56 who had no fracture. Information including histological diagnosis, anatomical site, radiographic appearance, severity of pain, and lesion size was recorded for the patients. A modified scoring system was proposed to predict the risk of fracture. RESULTS The univariate comparisons showed a significant difference between the fracture and non-fracture groups in terms of lesion type, pain, lesion-to-bone width, and axial cortical involvement of the patients (P < 0.05). Lesion type, pain, lesion-to-bone width, and axial cortical involvement were independently correlated with an increased risk of fracture. The mean score of the fracture group was 7.89, whereas the mean score of the non-fracture group was 6.01. The optimum cut-off value of the score to predict pathological fracture was 7. The scoring system had a sensitivity of 70% and a specificity of 80% for detecting patients with fractures. The Youden index was 0.5, which was the maximum value. The area under the receiver operator characteristic was 0.814. CONCLUSION Lesion type, pain, lesion-to-bone width, and axial cortical involvement are risk factors for pathological fracture. The modified scoring system can provide evidence for clinical decision-making in children with benign bone lesions. A bone lesion with a total score > 7 indicates a high risk of a pathologic fracture and is an indication for prophylactic internal fixation.