A method and apparatus for aligning the printing of dots generated by at least one array of printing elements in an printing apparatus, wherein the method includes the steps of printing a calibration test pattern, scanning the printed calibration test pattern, determining at least one calibration value based on the scanned calibration test pattern, positioning an alignment adjustment tool relative to the array of printing elements of which the alignment needs to be adjusted and, based on the calculated calibration value, automatically adjusting the alignment of the array of printing elements using the alignment adjustment tool.