Abstract: A method of calibrating a front to backside alignment capable lithographic apparatus. The method includes attaching a substrate having a plurality of alignment marks to a carrier, the substrate being arranged such that the alignment marks face towards the carrier; reducing the thickness of the substrate; using an alignment system of the apparatus to measure the positions of images of alignment marks formed by optics in a substrate table of the apparatus; projecting a pattern onto the substrate, the position of the pattern being determined according to the measured positions of the alignment marks; measuring the positions of the projected pattern and the alignment marks provided on the opposite side of the substrate, the position of the alignment marks provided on the opposite side of the substrate being measured by the alignment system directing radiation through the substrate; and comparing the measured positions in order to determine an overlay error.