Different types of novel wheat lines with different starch contents and amylose/amylopectin ratios, relating to defined alterations in the number and activity of starch synthase IIa genes, were processed by pilot-plant extrusion. Two types of products were produced: pure wholemeal products and breakfast cereals made from wholemeal/maize blends. Lower apparent shear viscosity was obtained in the extruder with lower starch content and higher amylose/amylopectin ratio flours (SSIIa-deficient line). The bulk density of the products decreased with increasing extrusion temperature and was always higher for the triple-null line. The bulk density was not completely explained by the melt shear viscosity, suggesting the importance of the fillers (fibers, brans) in the process of expansion and structure acquisition. The different mechanical properties were explained by the density and by the material constituting the cell walls. Enzyme-resistant starch (RS) content and hydrolysis index (HI) were not correlated to the extrusion temperature, but RS was higher in pure wholemeal products and in the SSIIa-deficient line. These results are discussed in terms of starch molecular architecture and product microstructure.