A method and apparatus for initializing an end-to-end link in a fiber optic communications system in which a pair of nodes interconnect a pair of end devices. A first node, upon initializing a device link segment with an end device to which the node is coupled, sends a signal to the other node over a network link segment indicating that the sending node has initialized its device link segment. The first node completes initialization of the end-to-end link upon receiving a signal from the other node over the network link segment indicating that the other node has initialized its device link segment. In an alternative initialization scheme, a node momentarily operates its data channel in a loopback mode to allow its end device to initialize the device link segment in accordance with a predetermined protocol before returning to a transparent mode.