The aim of the work was to investigate the effect of extrusion-cooking process conditions on the structure and pasting properties of starch extrudates. In addition, the extrudates structure was observed using scanning electron microscopy (SEM) and confocal laser microscopy (CSLM). Wheat, corn and potato starch were extrusion-cooked with different process parameters (moisture content, screw speed, process temperature) in a single screw extruder. Results showed influence of the process parameters on extruded starches pasting properties. Viscosity measurements indicated that water content during starch extrusion is more important than process temperature. The extrudates structure observed with scanning electron and confocal laser microscopes showed that the main effect of extrusion-cooking was loss of the crystalline structure of the starch and the formation of a cellular structure of the extrudates. In extrudates processed at higher starch moisture content reduced the quantity and diameters of created cells was observed.