A method to determine an overlay error between a first structure and a second structure, wherein the first structure and second structures are on different layers on a substrate and are imaged onto the substrate by a lithographic process, the method comprising: obtaining an apparent overlay error; obtaining a systematic error caused by a factor other than misalignment of the first and second structures; and determining the overlay error by removing the systematic error from the apparent overlay error. The method may alternatively comprise obtaining apparent characteristics of diffraction orders of diffraction by an overlapping portion of the first and second structures; obtaining corrected characteristics of the diffraction orders; determining the overlay error from the corrected characteristics; and adjusting a characteristic of the lithographic process based on the overlay error.