An imprint lithography apparatus is disclosed that has a substrate table configured to hold a substrate, a template holder configured to hold an imprint template, the imprint template or the template holder having a template alignment mark configured to be imprinted onto the substrate table or onto a substrate to form an imprinted alignment mark, the imprint template having a functional pattern, and the template alignment mark and the functional pattern having a known spatial relationship, and an alignment sensor configured to determine the location of the imprinted alignment mark.