Introduction: The purposes were to clarify the magnetic resonance imaging (MRI) findings of malignant ovarian lesions arising from endometriomas, and to compare the lesions' histopathology and MRI characteristics. Materials and Methods: Between May 2004 and December 2012, 140 patients, all of whom were diagnosed as having an endometrioma by using MR imaging, underwent surgery. We compared the MR characteristics including size and signal intensity of the tumor and mural nodules, the thickness of the septum, and the thickness of the wall with the pathological diagnoses. The attached angles of the mural nodules to the cyst wall were also evaluated. Results: Among the 179 lesions, preoperative MR imaging diagnosed 153 benign and 26 malignant. Based on the pathological results, 169 were diagnosed as benign and 10 were diagnosed as malignant. Finally, preoperative MR imaging correctly diagnosed 152 benign (group 1) and nine malignant (group 2), misdiagnosed 17 benign as malignant (group 3) and misdiagnosed one malignant as benign (group 4). As for mural nodules, there was a significant difference between groups 1 and 2 in the mean maximum diameter of the mural nodules. An acute attached angle was shown in 1 of 7 in group 1, in 11 of 16 in group 2, and in 14 of 22 in group 3. We also compared benign group with malignant group on the final pathological findings. As for mural nodules, there was a significant difference between groups 1 + 3 and group 2 in the mean maximum diameter of the mural nodules. On dynamic study, there were 22 enhanced mural nodules (75.9%) on group 1 + 3. Conclusion: Most of endometriomas preoperatively diagnosed as benign were pathological benign lesions. Endometriomas that contain many enhanced mural nodules with papillary shape, larger size, M. Kohno et al. 143 showing hypointense on T1WI, hyperintense on T2WI and showing an acute attached angle may have malignant potential.