Apparatus and techniques are disclosed for aligning the operation of the ink jet printhead cartridges of a multiple printhead ink jet swath printer that includes a print carriage that is movable along a horizontal carriage scan axis, (b) first and second ink jet printhead cartridges supported by the movable carriage for printing onto a print media that is selectively movable along a vertical media scan axis, and (c) an optical sensor supported by the movable carriage. Alignment of the operation of the printheads along the media scan axis is performed by determining with the optical sensor the relative positions of horizontal test line segments printed by selected nozzles of the printhead cartridges. The relative position information is utilized to calculate a vertical alignment correction which is implemented by enabling selected ink jet nozzles of the printheads and adjusting the position of one printhead cartridge relative to the other such that the nozzles of the ink jet printheads are properly spaced along the media scan axis.