OBJECTIVE: This study was undertaken to evaluate the immunoreactivity of progesterone receptor isoform B and nuclear factor kappa-B p65 subunit in ovarian endometrioma tissue samples harvested at the time of surgery and their relationship with the recurrence risk. STUDY DESIGN: One hundred nine patients were selected; 53 of them had recurrence within 30 months after surgery, whereas the other 56 had not had recurrence at least 32 months after surgery. For each patient, host and clinical information was also collected. The patients' archived, formalin-fixed, paraffin-embedded tissue blocks were retrieved, subjected to immunohistochemical staining of progesterone receptor isoform B and nuclear factor kappa-B p65 subunit, and were scored and compared. RESULTS: Increased nuclear factor kappa-B activation and decreased progesterone receptor isoform B immunoreactivity in ovarian endometriomas were 2 predominant factors in predicting recurrence. The classification tree method based on these 2 yielded a sensitivity of 86.6% and a specificity of 82.1%. CONCLUSION: Nuclear factor kappa-B activation/p65 and progesterone receptor isoform B immunoreactivity in ovarian endometrioma jointly constitutes a good biomarker for recurrence. The close relationship between nuclear factor kappa-B activation/p65 subunit and progesterone receptor isoform B immunoreactivity strongly suggests their roles involved in recurrence and may thus be excellent therapeutic targets to prevent recurrence. Our finding supports the notion that there are identifiable molecular genetic differences intrinsic to ovarian endometriomas that confer recurrence risk differential.