Non- and polysilsesquioxane-containing polyurethane-based powder coating systems, crosslinked with allophanate bonds containing polyisocyartates were examined. The surface structure built-up of the powder coatings were investigated at different temperatures with a polarized optical microscopy (POM) using reflected light. The three-dimensional surface topography and the values of surface roughness were determined. The surface structure was correlated with the chemical structure of the coatings and macroscopic surface behavior: surface free energy and gloss. These experimental results lead to a better understanding of the development of surface topography and morphology and provide valuable information for the development of new polyurethane powder coating systems. (C) 2010 Wiley Periodicals, Inc. I Appl Polym Sci 118: 3586-3593, 2010