Background: Preoperative differential diagnosis between atypical lipomatous tumor (ALT)/well-differentiated liposarcoma (WDLS) and lipoma is important to determine the appropriate resection margin. However, since their radiological and histopathological findings are similar, it may be difficult to make a differential diagnosis. In this study, we evaluated the diagnostic accuracies of clinical, radiological, and histopathological examinations for diagnosing ALT/WDLS and developed a new combined scoring system.Methods: Eighty-nine ALT/WDLS and 56 lipomas were included and their clinical characteristics, magnetic resonance imaging (MRI) findings, histological findings by hematoxylin and eosin (HE) staining were investigated, and compared between ALT/WDLS and lipoma. Then, univariate analyses and multivariate logistic regression analyses were performed for the findings, and a combined scoring system consisted of predictive factors of ALT/WDLS was developed. Results: The univariate and multivariate logistic regression analyses revealed that tumor location (lower extremity), deep site, and size (>11cm), thick septa (>2mm), enhancement of septa or nodular lesions on MRI, and lipoblasts in HE staining were significantly different for the diagnosis of ALT/WDLS. Based on the six predictive factors, we developed a combined scoring system (total 0–16 points, the cutoff was 9 points). The mean score of ALT/WDLS was significantly higher than lipoma (11.9 vs. 5.6, p<0.0001). The area under the curve was 0.945, and sensitivity was 87.6% and specificity was 91.1% by the receiver operating characteristics curve.Conclusions: We developed a new combined scoring system based on comprehensive examinations that excluded examination which requires special equipment and reagents such as fluorescence in situ hybridization (FISH), and this can be used in many medical institutions. The diagnostic accuracy of ALT/WDLS was high and it may be useful for preoperative diagnosis and surgical plan.