Techniques for increasing the safety of medical device programming using general purpose hardware, such as a general purpose personal computer, are described. Some embodiments include a watchdog module that is serviced by the general purpose hardware, a mediator module that monitors programming instructions from the general purpose hardware, and/or a safe mode input that may be activated by a user. In some embodiments, a system comprises an implantable medical device, an intermediate device, a computing device that communicates with the implantable medical device via the intermediate device. The intermediate device may provide any one or more of the safety measures described above. In some embodiments, the intermediate device is dedicated hardware, and critical programming functions are provided by the intermediate device, rather than the general purpose hardware. In some embodiments, an implantable medical device provides one or more of the above-discussed safety features, rather than a separate intermediate device.