In a method of determining the focus of a lithographic apparatus used in a lithographic process on a substrate, the lithographic process is used to form a structure on the substrate, the structure having at least one feature which has an asymmetry in the printed profile which varies as a function of the focus of the lithographic apparatus on the substrate. A first image of the periodic structure is formed and detected while illuminating the structure with a first beam of radiation. The first image is formed using a first part of non-zero order diffracted radiation. A second image of the periodic structure is formed and detected while illuminating the structure with a second beam of radiation. The second image is formed using a second part of the non-zero order diffracted radiation which is symmetrically opposite to the first part in a diffraction spectrum. The ratio of the intensities of the measured first and second portions of the spectra is determined and used to determine the asymmetry in the profile of the periodic structure and/or to provide an indication of the focus on the substrate. In the same instrument, an intensity variation across the detected portion is determined as a measure of process-induced variation across the structure. A region of the structure with unwanted process variation can be identified and excluded from a measurement of the structure.