Endometriosis is one of the most common benign gynaecologic diseases and its clinical presentation is generally ovarian endometrioma. We aimed to assess the association of tumour markers with histopathological structure of ovarian endometriomas to assess their roles in clinical management. Data from 86 women who underwent laparoscopic surgery for ovarian endometrioma were evaluated. The possible risk factors for inadvertently removed normal ovarian parenchyma (IRNOP) during laparoscopic cystectomy and the relationship between tumour markers and histopathologic parameters of ovarian endometrioma were assessed. Age and the depth of penetration of endometrial tissue into the cyst wall showed a significant positive correlation with thickness of IRNOP. There was a significant negative correlation between IRNOP and the thickness of fibrosis on cyst wall. Thickness of fibrosis and the depth of penetration represented significant positive correlations with tumour markers (CA 125, CA 15-3, and CA 19-9), respectively. This is the first study that reveals the association between tumour markers and the histopathologic features of ovarian endometrioma. The outcome of the present study indicated that lower levels of tumour markers may permit a conservative management, rising levels may help in timing of a possible surgical intervention and high levels may help in counselling postoperative outcomes.Impact statement What is already known on this subject?Endometriosis is defined as a benign gynaecologic disease, and the vast majority of women who suffer from endometriosis are of reproductive age. Ovarian endometriotic cysts are found in one-fifth to one-half of patients with endometriosis. Laparoscopic cystectomy is accepted as the gold standard for the surgical management of ovarian endometriotic cysts because of the procedure's several clinical advantages, such as lower recurrence and higher pregnancy rates. However, studies have indicated that laparoscopic excision of an ovarian endometrioma capsule could be associated with a reduction in both the ovarian volume and the follicle count. What do the results of this study add?Our retrospective data indicate that tumour markers may have role in planning the management of ovarian endometriomas. What are the implications of these findings for clinical practice and/or further research?Low tumour markers levels may permit a conservative management, elevating levels may help in timing of a possible surgical intervention and finally high levels may help in counselling the patient about her possible postoperative outcomes.