Endometriosis is a common gynecologic disorder histologically characterized by the displacement of endometrial tissue to extra-uterine locations. A significant cause of infertility and pelvic pain, the global socioeconomic burden of endometriosis is staggering. Laparoscopy remains the gold standard for the diagnosis of the condition. However, the invasive nature of surgery, coupled with the lack of a laboratory biomarker for the disease, results in a mean latency of 6-7 years from onset of symptoms to definitive diagnosis. Unfortunately, the delay in diagnosis may have significant consequences in terms of disease progression. The discovery of a sufficiently sensitive and specific biomarker for the non-surgical detection of endometriosis promises earlier diagnosis and prevention of deleterious sequelae, and remains a top research priority. The enigmatic pathophysiology of endometriosis presents unique challenges to biomarker development that are now well outlined. Within the past decade, significant advancements in understanding the molecular hallmarks of endometriosis have occurred, and promising biomarker candidates are emerging.