Methods of manufacturing an integrated circuit by a lithographic apparatus are disclosed. The methods include patterning a radiation beam with a patterning device, projecting the patterned beam onto a substrate using a projection system, and determining the position of the patterning device. In one example, the patterning device's position relative to the projection system is determined by measuring the position of the patterning device's support structure. In another example, the position can be determined by measuring a position of the patterning device relative to its support and by measuring a position of the support. In another example, a Z-position of the patterning device is determined by directing at least one beam of radiation onto a part of the patterning device located outside a pattern area. This can be done by directing a pair of laser beams from sensors on the projection system to reflecting strips on the patterning device.