A lithographic apparatus equipped with an improved alignment system, is presented herein. In one embodiment, the apparatus includes a radiation system for providing a projection beam of radiation, a support structure for supporting a patterning device that configures the projection beam according to a desired pattern, a substrate holder for holding a substrate, projection system for projecting the patterned beam onto a target portion of the substrate, and an alignment system. The alignment system includes a radiation source for illuminating at least one mark which is usable for alignment on a substrate and an imaging system for imaging light which has interacted with the at least one mark to generate alignment information.