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Background: Discrimination between benign and atypical lipomatous tumors (ALT) is important due to potential local complications and recurrence of ALT but can be difficult due to the often-similar imaging appearance. Using a standardized MRI protocol, this study aimed to rank established and quantitative MRI features by diagnostic value in the differentiation of benign and atypical lipomatous tumors and to develop a robust scoring system. Methods: Patients with clinical or sonographic suspicion of a lipomatous tumor were prospectively and consecutively enrolled from 2015 to 2019 after ethic review board approval. Histology was confirmed for all ALT and 85% of the benign cases. Twenty-one demographic and morphologic and twenty-three quantitative features were extracted from a standardized MRI protocol (T1/T2-proton-density-weighting, turbo-inversion recovery magnitude, T2* multi-echo gradient-echo imaging, qDIXON-Vibe fat-quantification, T1 relaxometry, T1 mapping, diffusion-weighted and post-contrast sequences). A ranking of these features was generated through a Bayes network analysis with gain-ratio feature evaluation. Results: Forty-five patients were included in the analysis (mean age, 61.2 ± 14.2 years, 27 women [60.0%]). The highest-ranked ALT predictors were septation thickness (gain ratio merit [GRM] 0.623 ± 0.025, <i>p</i> = 0.0055), intra- and peritumoral STIR signal discrepancy (GRM 0.458 ± 0.046, <i>p</i> < 0.0001), orthogonal diameter (GRM 0.554 ± 0.188, <i>p</i> = 0.0013), contrast enhancement (GRM 0.235 ± 0.015, <i>p</i> = 0.0010) and maximum diameter (GRM 0.221 ± 0.075, <i>p</i> = 0.0009). The quantitative features did not provide a significant discriminatory value. The highest-ranked predictors were used to generate a five-tiered score for the identification of ALTs (correct classification rate 95.7% at a cut-off of three positive items, sensitivity 100.0%, specificity 94.9%, likelihood ratio 19.5). Conclusions: Several single MRI features have a substantial diagnostic value in the identification of ALT, yet a multiparametric approach by a simple combination algorithm may support radiologists in the identification of lipomatous tumors in need for further histological assessment.