Carbon in various forms is widely used as catalyst and catalyst support. The microstructure plays an essential role in determining the properties of carbon materials. In the past, different attempts have been made to elucidate the interrelation between structure (geometrical and electronic) and reactivity of these materials. The invention of scanning tunneling microscopy (STM) provided new opportunities to study such interdependences in more detail. In this paper, we review STM studies on carbon materials used in catalysis and discuss possibilities and limitations of scanning probe microscopy (SPM) techniques in the characterization of these materials.