A lithographic apparatus including a support to support a patterning device, a substrate table to hold a substrate, and a projection system to project a radiation beam patterned by the patterning device onto a target portion of the substrate. A transparent layer is provided to protect the pattering device. The apparatus further includes a transparent layer deformation-determining device to determine a deformation profile of the transparent layer, the deformation profile of the transparent layer expressing a deformation of the transparent layer during a scanning movement of the lithographic apparatus, and a compensator device which is configured to control the projection system, the substrate table and/or the support in response to the deformation profile of the transparent layer to compensate for the deformation of the transparent layer during the scanning movement of the apparatus.