A method of patterning substrates using a lithographic apparatus. The method comprising providing a beam of radiation using an illumination system, using a patterning device to impart the radiation beam with a pattern in its cross-section, and using a projection system to project the patterned radiation beam onto target portions of a lot of substrates, wherein the method further comprises performing a radiation beam aberration measurement after projecting the patterned radiation beam onto a subset of the lot of substrates, performing an adjustment of the projection system using the results of the radiation beam aberration measurement, then projecting the patterned radiation beam onto a further subset of the lot of substrates.