Calibration of an angularly resolved scatterometer is performed by measuring a target in two or more different arrangements. The different arrangements cause radiation being measured in an outgoing direction to be different combinations of radiation illuminating the target from ingoing directions. A reference mirror measurement may also be performed. The measurements and modeling of the difference between the first and second arrangements is used to estimate separately properties of the ingoing and outgoing optical systems. The modeling may account for symmetry of the respective periodic target. The modeling typically accounts for polarizing effects of the ingoing optical elements, the outgoing optical elements and the respective periodic target. The polarizing effects may be described in the modeling by Jones calculus or Mueller calculus. The modeling may include a parameterization in terms of basis functions such as Zernike polynomials.