An improved medical device system is disclosed in which system devices communicate optically. An Implantable Medical Device (IMD) is disclosed having a hermetic window assembly on one side of its case, through which a photoemitter and photodetector can transmit and receive optical signals. The optical radiation in the signals is preferably visible, which permits communications from the IMD to be seen prior to implantation and even after implantation through a patient's tissue. External controllers for adjusting therapeutic operation of the IMD, external chargers for providing a magnetic charging field to charge a battery in the IMD, and combined external controllers/chargers are also disclosed that optically communicate with the IMD through the patient's tissue. The optical communication capabilities of the external charger are particularly useful in determining misalignment with the IMD.