A method and system are provided for aligning signals in a communication system. The method and system include alignment logic or functionality configured to compensate for signal propagation discrepancies when communicating signals between one or more other devices. The alignment logic may operate to adjust one or more communicated signals, so that signals that may have different propagation times arrive at one or more devices at a desired time. The system and method may be used when initializing a communication system and before communicating data. The system and method operate to adjust one or more signals, such as a data strobe signal in a memory system for example, so that the one or more signals arrive at one or more devices spaced apart in time within a defined tolerance at a desired time. The alignment logic is used to compensate for signal propagation delays which can be associated with a signal propagation path.