A method to determine a rotation of a substrate with respect to the patterning device without using a reference mark on the substrate is presented. At least two structures having corresponding features and present on the substrate, e.g. previously projected patterns, are imaged with a known position with respect to a measurement coordinate system. A distance vector between the at least two structures is determined. From the distance vector, a rotation angle is calculated. In an embodiment of the invention, there is provided a method to estimate a position of the substrate from the acquired image(s). A position is measured and used as a reference position for subsequent substrates of which the rotation angle is to be determined.