A method of projecting an image onto a plurality of target areas on a substrate whereby use is made of a lithographic projection apparatus comprising: a radiation system for supplying a projection beam of radiation; a mask table provided with a mask holder for holding a mask; a substrate table provided with a substrate holder for holding a substrate; a projection system for imaging an irradiated portion of the mask onto a target area of the substrate, whereby the substrate is to be irradiated with images from at least two different masks, characterized by the following steps: (a) providing a batch of substrates, each at least partially coated with a layer of radiation-sensitive material; (b) providing storage means for temporary storage of the batch; (c) providing a first mask on the mask table; (d) irradiating a first set of target areas of a first substrate with an image from the first mask, and then placing that substrate in the storage means; (e) repeating step (d) for each of the other substrates in the batch; (f) replacing the first mask by a second mask; (g) providing a primary substrate from the storage means on the substrate table and irradiating a second set of target areas of that substrate with an image from the second mask; (h) repeating step (g) for each of the other substrates stored in the storage means.