A centralized management system for medical devices includes a network, a central server coupled to the network, and a medical device programmer coupled to the network. The central server includes at least one prescription system for prescribing at least one programmable parameter of a medical device based on at least one characteristic of a patient. The medical device programmer communicates at least one characteristic of a patient to the central server via the network, receives at least one parameter from the central server via the network, and programs the medical device using the at least one parameter. In one embodiment, the central server hosts expert prescription systems defined by multiple experts, and a user selects one of the expert prescription systems. In another embodiment, the central server hosts a custom prescription system defined by the user.