Endometriosis is a condition defined by the presence of endometrial glands and stroma in ectopic locations. While the most commonly seen symptoms of the disease are pelvic pain, dysmenorrhea, and infertility, endometriosis has also systemic effects in multiple organ systems. Here, we review literature describing closely associated comorbidities including cardiovascular disease, cancers, autoimmune disease, psychiatric conditions, and metabolism/body weight. We examine the pathophysiology and hypothesized mechanism by which endometriosis may lead to these systemic effects; mechanisms include cytokine and micro-RNA production as well as stem cell migration and dissemination. The broad systemic effects of endometriosis as well as correlated comorbidities are often overlooked in the treatment of patients with endometriosis. Increased awareness may lead to more effective treatment and prevention.