In an illumination system (12, 13) for a scatterometer, first and second spatial light modulators lie in a common plane and are formed by different portions of a single liquid crystal cell (260). Pre-polarizers (250) apply polarization to first and second radiation prior to the spatial light modulators. A first spatial light modulator (236-S) varies a polarization state of the first radiation in accordance with a first programmable pattern. Second spatial light modulator (236-P) varies a polarization state of the second radiation accordance with a second programmable pattern. A polarizing beam splitter (234) selectively transmits each of the spatially modulated first and second radiation to a common output path, depending on the polarization state of the radiation. In an embodiment, functions of pre-polarizers are performed by the polarizing beam splitter.