A system and method is provided for characterizing color separation misregistration associated with marking a substrate. The method includes providing an input image having a plurality of patches, each patch having a pattern using a first and second color; marking a substrate with a copy of the input image using a first and second color separation to correspond to the first and second colors, respectively; and measuring a color characteristic of markings of respective copied patches of the copied plurality of patches and generating corresponding colorimetric values. Misregistration of the first color separation markings relative to the second color separation markings is characterized based on the measured calorimetric values.