Objective: To evaluate the adverse effects of endometriomas on ovarian reserve. Design: Analysis of prospectively collected biopsy samples. Setting: Gynecology research unit in a university hospital. Patient(s): Women younger than age 35 years with endometriomas. Intervention(s): Biopsy of normal cortex from ovaries affected by endometriomas (≤4 cm) and contralateral ovaries without cysts. Main Outcome Measure(s): Presence of cortex-specific stroma, observation of superficial endometriosis, follicular density, and presence of fibrosis. Result(s): Twenty samples of cortical tissue from ovaries with endometriomas and 11 from contralateral ovaries without cysts were analyzed. Follicular density was significantly lower in cortex from ovaries with endometriomas than in cortex from contralateral ovaries without cysts (mean ± SD = 6.3 ± 4.1/mm3 vs 25.1 ± 15.0/mm3). Eleven (55%) cortical samples from ovaries with endometriomas showed fibrosis and concomitant loss of cortex-specific stroma, not observed in contralateral normal ovaries. Multivariate analysis revealed that the presence of endometrioma and fibrosis were significantly and independently associated with follicular density. Conclusion(s): Endometriotic cyst formation and associated structural tissue alterations in apparently normal ovarian cortex may be a cause of reduced ovarian reserve. Early diagnosis and intervention may be beneficial in women with endometriomas to protect their ovarian function. [Copyright &y& Elsevier]