Recent studies have focused on the role of oxidative stress, which may be implicated in the development, progression, and pathophysiology of endometriosis. The aim of this study is to investigate the redox balance of endometriosis by simultaneously measuring iron-related compounds (total iron, heme iron, free iron, oxyhemoglobin [oxyHb], methemoglobin [metHb] and 8-hydroxy-2-deoxy guanosine [8-OHdG]) and antioxidants (bilirubin, heme oxygenase-1 [HO-1] and total antioxidant capacity [TAC]). This study includes 236 histopathologically confirmed cases (178 cases of endometriosis and 58 cases of non-endometriosis). Cyst fluid samples were collected from patients admitted to the Department of Gynecology, Nara Medical University, Kashihara, Japan, for surgery. Age at diagnosis (p <0.001), the maximum diameter of the cyst (p <0.001) and CA125 levels (p <0.001) differed significantly between the two groups. Total iron, heme iron, free iron, metHb, and oxyHb were markedly higher in endometriosis compared to non-endometriosis. Bilirubin, HO-1 and TAC were significantly higher in endometriosis patients compared with those from non-endometriosis patients. In endometriosis, total iron showed a positive correlation with HO-1 (r, 0.518, p = 0.001), but there were no antioxidants that correlated with iron in non-endometriosis. Iron and HO-1 did not correlate with age or tumor size. HO-1 may regulate the delicate balance of iron-induced oxidative stress in endometriotic cyst fluid.