An implantable medical device system for orientation-independent telemetry to and from the device are disclosed. The system includes an external controller which produces an electromagnetic field to induce a current in a coil in the implantable medical device and vise versa. In a preferred embodiment, the external controller comprises three orthogonal coils, each of which is potentially activated to generate or receive the electromagnetic field. Algorithms are disclosed to allow for the choice of one or more of the coils best suited for telemetry based on the chosen coil's orientation with respect to the telemetry coil in the implantable medical device. Because all three of the orthogonal coils are potentially activated if necessary, the result is that at least one of the coils will be in a proper orientation with respect to the coil in the implantable medical device, thereby improving telemetry or power transfer efficiency.