A system and method for assessing link quality for radio frequency (RF) transmissions between a programmer and an implantable medical device (IMD) is provided. An embodiment of the method includes measuring a plurality of available wireless communication channel potentially used to communicate between an implantable medical device (IMD) and a programmer to determine signal and noise levels for the channels. The method also includes storing the signal and noise levels. The method further includes processing the stored levels to determine the interference potential on the channels adjacent to the available channels. In this embodiment, the method also includes selecting a preferred communication channel based on a function of noise level for a target center channel and interference potential for corresponding adjacent channels to the target channel. Other aspects and embodiments are provided herein.