The aim of the study was to evaluate apoptosis through regulation of Bcl-2, Bax and Mcl-1 proteins by comparing their expressions in endometriotic cyst lesions and the endometrium of the patients with moderate to severe endometriosis. This is a cross-sectional study of 30 women in reproductive age with a clinical or sonographic suspicion of endometrioma, who underwent laparoscopy. Bcl-2 expression was positive both in cystic endometriotic lesions and endometrium, and its expression was significantly reduced in the cystic endometriotic lesions (p < 0.0001). There was a significant difference in Bcl-2 expression between cystic endometriotic stromal cells and endometrial stromal cells (p < 0.0001). Bax expression was positive both in cystic endometriotic lesions and endometrium, and its expression was significantly lower in the endometrium (p < 0.0001). There was a significant difference in Bax expression between cystic endometriotic stromal cells and endometrial stromal cells (p = 0.03). Mcl-1 expression was positive both in cystic endometriotic lesions and endometrium, and its expression was significantly lower in the cystic endometriotic lesions (p = 0.003). Apoptosis may play a role in the pathophysiology of endometriosis by potentially contributing to the survival of regurgitating endometrial cells in the peritoneal cavity.