A control system is provided for controlling a support structure in a lithographic apparatus. The control system includes a first measurement system arranged to measure the position of a substrate supported by the support structure, the position being measured in a first coordinate system. The control system further includes a second measurement system for measuring the position of the support structure in a second coordinate system, the first measurement system having a presumed position in the second coordinate system. The control system further comprises a controller configured to control the position of the support structure based on measurements by the second measurement system, to convert the measured position of the substrate into a converted position of the support structure in the second coordinate system, to position the support structure based on the converted position, to receive a position error signal indicative of a difference between the presumed position and an actual position of the first measurement system in the second coordinate system, and to position the support structure in a manner dependent upon the position error signal.