A method and apparatus for retraining skew compensation in an interface is presented. In one embodiment, a retraining interval is determined, and counters in the transmitting agent and receiving agent count up until the retraining interval is reached. A tracking unit used to select one of several interpolated clocks may then be powered up, and a special retraining phit may be sent across the interface. During the retraining process, the transfer of flits into and out of the flow-control mechanism may be inhibited. When the retraining process is finished, the tracking unit may be powered down.