This mini-review summarizes the different pain-associated diseases and potential mechanisms that may help to achieve a deeper understanding of gender differences presented in clinical aspects of the functional syndromes. Chronic visceral pain is the most common complication of many functional disorders that do not have a defined pathophysiological cause. Functional pain syndromes include common disorders such as Irritable Bowel Syndrome (Gastroenterology), Interstitial Cystitis/Painful Bladder Syndrome (Urology), Fibromyalgia (Rheumatology), and Chronic Pelvic Pain (Gynecology) and cross multiple medical disciplines. Patients suffering from functional diseases may progress to cognitive decline and depression through neuroplastic changes not only at the level of central nervous system but also in the periphery. Pain pathways are activated in virtually all human diseases and only a thorough understanding of the mechanism implicated in the functional, painful disorders can truly contribute to more efficient therapeutic interventions.