The mammalian kidney is responsible for a multitude of homeostatic functions, which are mediated by both structural and functional diversity along the renal tubule. In this article, we focus on the major functions of the terminal portion of the renal tubule, the medullary collecting duct system. The role of the medullary collecting ducts in determining the composition of the final urine through controlled water, sodium, chloride, potassium and urea reabsorption, ammonia transport, and acid-base homeostasis is discussed. The molecular identity of the major channels and transporters that contribute to medullary collecting duct function are described in detail, including; aquaporins, urea transporters, the epithelial sodium channel (ENaC), the Na,K-ATPase, H-ATPase, Rh glycoproteins, and sodium bicarbonate transporters. Knowledge gained from studies in knockout mice is also discussed.