A system and method for measuring, monitoring and mitigating EMI interference in an implanted stimulation lead system associated with an IPG. A Kelvin connection scheme operative with a diagnostic circuit is provided for sensing an interference voltage induced at a Kelvin connect electrode of the lead system, wherein the diagnostic circuit is configured to generate one or more control signals for adjusting in substantially real time a common-mode voltage reference provided to supply a biasing voltage to the IPG circuitry.