The operational requirements of the National Ignition Facility place tight constraints upon its alignment system. In general, the alignment system must establish and maintain the correct relationships between beam position, beam angle, laser component clear apertures, and the target. At the target, this includes adjustment of beam focus to obtain the correct spot size. This must be accomplished for all beamlines in the time consistent with planned shot rates and yet, in the front end and main laser, beam control functions cannot be initiated until the amplifiers have sufficiently cooled so as to minimize dynamic thermal distortions during and after alignment and wavefront optimization. The scope of the task dictates an automated system that implements parallel processes. We describe reticle choices and other alignment references, insertion of alignment beams, principles of operation of the Chamber Center Reference System and Target Alignment Sensor, and the anticipated alignment sequence that will occur between shots.