PURPOSE: To investigate magnetic resonance (MR) findings and to detect malignant transformation of ovarian endometriotic cysts by comparing longitudinal changes in patients with ovarian malignant/borderline tumors associated with ovarian endometriotic cysts (tumor group) with those of patients with endometriotic cysts (control group). METHODS: Tumor group patients (n = 10) had ovarian malignant/borderline tumors with pathologically confirmed association with endometriosis and available prior MRI of endometriotic cysts. Control group patients (n = 40) had been diagnosed more than two times as having ovarian endometriotic cysts by MRI examination. The tumor and solid portion sizes were measured. Two radiologists independently evaluated signal intensity (SI) of the cystic portion on both T1-weighted and T2-weighted images (WI), presence of shading on T2WI, and T2 dark spot sign in both groups and evaluate longitudinal changes of those findings. RESULTS: Pathological diagnoses of the tumor group were clear cell carcinoma (n = 6), endometrioid carcinoma (n = 1), serous carcinoma (n = 1), mucinous borderline tumor (n = 1), and endometrioid borderline tumor (n = 1). Tumor size had increased significantly in the tumor group (p = .004), but not in controls. Solid portions were identified in all cases only when neoplasms were suspected. Disappearance of shading during the follow-up period was observed more in tumor group (n = 2) than in the controls (n = 0). No significant difference was found between groups in the SI on T1 and T2WI, and T2 dark spot sign for the two MR examinations. CONCLUSIONS: The MR findings suggesting malignant transformation were emergence of a solid portion and increase in cyst size. Disappearance of shading also facilitates the follow-up of endometriotic cysts.