A method for effecting an in-band reset of the physical layers of two agents interconnected through a link-based interconnection scheme. In accordance with one embodiment of the invention, a first of the two agents ceases its forwarded clock to initiate the in-band reset. Upon realization of the cessation, a second agent ceases its forwarded clock and proceeds to a reset state. The first agent then proceeds to a reset state. Subsequently, after waiting a specified period of time, both agents proceed with a re-initialization of the physical layer. In accordance with one embodiment of the invention, the re-initialization of the physical layer is effected without impacting other layers of the interconnection hierarchy.