A pacemaker system is provided which provides for more flexibility in re-programming of the control software, or program which is controlling an implanted pacemaker. The system comprises an external programmer device which is capable both of programming the implanted device in a conventional way, and also downloading new control software to the implanted device, subject to predetermined system conditions. All implanted devices, e.g., pacemakers within the system of the invention, share a hardware platform, and are identified as belonging to a given one of a plurality of groups, each group being characterized as providing therapy aimed at a different condition. Each pacemaker also carries type data, indicating the type of pacemaker within the group, and a set of permissions data representative of different types within the group to which it is permitted to be programmed. Upon interrogating the implanted device, the programmer determines whether the device is part of the system, what its group and type is, and whether it is able to modify the device.