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Endometriosis is a chronic disease with the potential to cause devastating clinical manifestations such as infertility and chronic pelvic disease. Current treatment is limited to surgical intervention and pharmacologic therapy targeting estrogen and progesterone to suppress ectopic endometrial tissue proliferation. Undesired side effects and contraindications to the use of hormonal medications may reduce treatment options. As the pathogenesis of endometriosis continues to be investigated, new therapies will emerge. The identification of genes involved in the development of endometriosis may allow targeted therapy to prevent or cure disease. In addition, increasing knowledge of the inflammatory pathways that promote ectopic endometrial growth will permit the development of pharmacologic agents to manipulate these signaling pathways. Utilization of selective progesterone receptor modulators, aromatase inhibitors, and modern gonadotropin-releasing hormone antagonists provide more options to manage disease when traditional treatment fails. Individualized therapeutic strategies will soon be a reality as a greater understanding of endometriosis is obtained through the investigation of genomic studies, molecular pathways, and environmental influences.