Systems and methods for programming and logging medical device and patient data are provided. The systems include a handheld device, which is capable of communicating with a medical device, and a base station, which provides connectivity for the handheld device to accomplish various functions such as recharging, programming, data back-up and data entry. The methods comprise the steps of detecting a medical device, obtaining and recording information from the medical device. Additionally, medical device parameters may be modified and the recorded information may be archived for future reference.