The differentiation between the atypical cartilaginous tumor (ACT) and the enchondromas is crucial as ACTs require a curettage and clinical as well as imaging follow-ups, whereas in the majority of cases enchondromas require neither a treatment nor follow-ups. Differentiating enchondromas from ACTs radiologically remains challenging. Therefore, this study evaluated imaging criteria in a combination of computed tomography (CT) and magnetic resonance (MR) imaging for the differentiation between enchondromas and ACTs in long bones. A total of 82 patients who presented consecutively at our institution with either an ACT (23, age 52.7 ±18.8 years; 14 women) or an enchondroma (59, age 46.0 ± 11.1 years; 37 women) over a period of 10 years, who had undergone preoperative MR and CT imaging and subsequent biopsy or/and surgical removal, were included in this study. A histopathological diagnosis was available in all cases. Two experienced radiologists evaluated several imaging criteria on CT and MR images. Likelihood of an ACT was significantly increased if either edema within the bone (p = 0.049), within the adjacent soft tissue (p = 0.006) or continuous growth pattern (p = 0.077) were present or if the fat entrapment (p = 0.027) was absent on MR images. Analyzing imaging features on CT, the likelihood of the diagnosis of an ACT was significantly increased if endosteal scalloping >2/3 (p < 0.001), cortical penetration (p < 0.001) and expansion of bone (p = 0.002) were present and if matrix calcifications were observed in less than 1/3 of the tumor (p = 0.013). All other imaging criteria evaluated showed no significant influence on likelihood of ACT or enchondroma (p > 0.05). In conclusion, both CT and MR imaging show suggestive signs which can help to adequately differentiate enchondromas from ACTs in long bones and therefore can improve diagnostics and consequently patient management. Nevertheless, these features are rare and a combination of CT and MR imaging features did not improve the diagnostic performance substantially.