OBJECTIVE: Endometriosis is a chronic, estrogen dependent condition that affects 5-10% of reproductive aged women and is associated with pelvic pain and infertility. As the approach to therapy shifts from surgical ablation to pharmacological control, a non-surgical mode of diagnosis would be desirable. The ENDOmarker study was designed by the NICHD Reproductive Medicine Network (RMN) to obtain well characterized and phenotyped bio specimens in a standardized fashion from women with and without endometriosis. DESIGN: Development of a diagnostic test. SETTING: Academic medical centers. PATIENTS: This study will enroll up to 500 participants, and follow them for up to 5 months. Included subjects are aged 18-44, scheduled to undergo gynecologic surgery (laparoscopy/laparotomy) for clinical reasons. INTERVENTIONS: Presence and stage of endometriosis (or its absence) is characterized by visual examination at the time of surgery. Subjects will undergo extensive clinical evaluation pre-operatively and at visits one and four months postoperatively. Endometrial biopsy, blood, urine and disease specific questionnaires will be collected at each visit. MAIN OUTCOME: Samples will be placed in a bio-repository to be used to validate and optimize the clinical use of genomic classifiers of the endometrium alone or in combination with serum cytokines as a non-surgical composite marker of endometriosis. CONCLUSION: This protocol can serve as a reference for objective collection of high quality bio specimens for discovery or validation of potential nonsurgical diagnosis of presence or severity of disease.