Recent developments of element-specific microscopy techniques using synchrotron radiation are opening new opportunities for the analytical investigation of various heterogeneous materials. This article provides a general description of the operational principles of different microscopes allowing chemical and structural imaging combined with micro-spot spectroscopic analysis. Several selected examples are used to illustrate the potential of the synchrotron-based methods in terms of imaging and chemical sensitivity for identification of spatial variations in the composition of morphologically complex and nano-structured inorganic and organic materials, including biological samples.