The aims of this study were to evaluate the clinical characteristics and recurrence rate of atypical endometriosis (AE) 1 compared to typical endometriosis (TE) in addition to the malignant transformation rate among a large cohort. Study design: The medical records of 2681 patients who had undergone surgical treatment of ovarian endometrioma between January 2008 and September 2019 were retrospectively reviewed. The patients were divided into AE (n = 86) and TE (n = 2595) groups. Patients' characteristics and recurrence rates were evaluated and compared between the two groups. Results: The mean size of ovarian cysts was significantly larger in the AE group (7.6 AE 3.5 cm vs 6.7 AE 3.3 cm, p = 0.01) and the proportion of nulliparous women was significantly lower in AE group (65.1 % vs 77.8 %, p = 0.008). Otherwise, there were no statistically significant differences in patient characteristics between the two groups. After Cox regression analyses with IPTW was adjusted, the risk factors for recurrent endometrioma were higher preoperative CA125 level >48 U/mL (hazard ratio [HR] = 2.741; 95 % confidence interval [CI] = 1.517À4.952; p < 0.001), multilocular cyst (HR = 1.909; 95 % CI = 1.128À3.230; p = 0.016), and atypical endometriosis (HR = 2.666; 95 % CI = 1.659À4.284; p < 0.001). The AE group displayed a significantly higher cumulative recurrence rate than the TE group (p = 0.0057, log-rank test). No patients were diagnosed with atypical endometriosis to malignant transformation during the follow-up periods. However, two typical endometriosis patients experienced borderline malignancy and serous carcinoma, respectively. Conclusion: Recurrence rates for AE were higher than for TE. Although the AE group included no patient with malignant transformation in this study, considering the higher recurrence as well as the possibility of malignant transformation, long-term close surveillance is warranted.