This article summarizes key issues for future research on borderline ovarian tumors that emerged at a National Cancer Institute-sponsored Borderline Ovarian Tumor Workshop held in August 2003 in Bethesda, MD. Limitations in existing research and opportunities for future advances have been highlighted. The application of new molecular techniques in combination with improved study designs holds promise for elucidating the pathogenesis of these tumors and revealing the source of the extra-ovarian lesions ("implants") with which they are frequently associated. Clarification of the etiology of borderline tumors and the pathogenesis of their associated implants is critical for improving pathological diagnosis, revising the classification system of ovarian neoplasms, and developing optimal, evidence-based clinical management algorithms.