The causes of infertility in women with endometriosis may range from anatomical distortions to various pathophysiological disturbances. The aim of the present study was to examine the effects of the cyst fluid (CF) concentration of iron on infertility in patients with ovarian endometrioma (OMA). Patients with histologically confirmed OMA were enrolled at the Department of Obstetrics and Gynecology, Nara Medical University Hospital between 2013 and 2019. The patients were divided into 2 groups, namely women experiencing current infertility (infertile group) and those without complaints of infertility (non-infertile group). There were 2 types of patients in the infertile group: Patients who failed to achieve a clinical pregnancy following ≥12 months of regular unprotected sexual intercourse and those who had already been treated at fertility clinics. The CF concentration of iron was measured by the inductively coupled plasma-optical emission spectrometry (ICP-OES) method. The clinical data were analyzed retrospectively. A total of 77 patients were enrolled in the present study. Among these, 32 (41.6%) patients had infertility. When compared with the non-infertile women, the infertile women were significantly younger (median age, 35 years; range, 24-47 years; vs. median age, 40 years; range, 21-53 years; respectively; P=0.003). The CF concentrations of iron (median, 324.8 mg/l; range, 71.3-1046.3 mg/l; vs. median, 226.5 mg/l; range, 65.3-737.5 mg/l; respectively; P=0.019) were significantly higher in the infertile group compared with the non-infertile group. Multivariate logistic regression analysis indicated that age at diagnosis (≤38 years), the CF concentrations of iron (>326.6 mg/l) and the infertility index (iron/age ratio, >8.37) were independent risk factors for endometriosis-related infertility. Multivariate analysis revealed that age (HR, 6.44; 95% CI, 2.06-20.12) and iron (HR, 4.90; 95% CI, were independent factors for the identification of patients with OMA who presented with a complaint of infertility. In addition, the infertility index (iron/age ratio, >8.37; HR, 4.85; 95% CI, 1.01-23.27) was an important predictor of infertility. ROC curve analysis also revealed that the areas under the ROC (AUC) for age, iron and infertility index were 0.699, 0.666 and 0.731, respectively. On the whole, the findings of the present study demonstrate that age at diagnosis and the CF concentration of iron may be potentially effective markers for predicting infertility in women with OMA.