A medical instrument including a probe adapted to be inserted into an orifice of an animal's body. The instrument includes an emitter of electromagnetic radiation that is sensed by a sensor mounted on the probe. The sensor can then determine, by variations in the amount of radiation received from the emitter, whether a probe cover is mounted over the probe. A sensor can also be used to determine whether the walls of the body orifice block the radiation received from the emitter, thereby indicating position of the sensor, and thus, the probe within the orifice. A special probe cover is disclosed, and methods of using the medical instrument are also disclosed.