A method and circuit for implementing lane shuffle for fault-tolerant communication links, and a design structure on which the subject circuit resides are provided. Shuffle hardware logic steers a set of virtual data lanes onto a set of physical optical lanes, steering around all lanes that are detected as bad during link initialization training. A mask status register is loaded with a mask of lane fail information during link training, which flags the bad lanes, if any. The shuffle hardware logic uses a shift template, where each position in the starting template is a value representing the corresponding lane position. The shift template is cascaded through a set of shifters controlled by the fail mask.