Deformation-induced modification of the dispersion state of silica nanoparticles in poly(ethylene terephthalate) (PET) has been characterized by means of transmission electron microscopy (TEM) and wide-angle X-ray diffraction (WAXD). We focused on the biaxial deformation applied at a temperature just above the glass transition temperature (110 degrees C), during the free stretch-blowing process of amorphous PET modified with submicron silica. The first nanocomposite studied contains 2.5 wt % of fractal aggregated pyrogenic silica. The particles are well dispersed after the polymerization of PET, but they agglomerate and orient strongly parallel to the elongation direction after biaxial deformation. They form long streams of particles (> 2 mu m long) regularly spaced by a distance of 50-100 nm. Interestingly, the silica organization is consistent with the hierarchical structure commonly proposed for the strain-induced crystallization of PET. The particles are rejected from the highly oriented domains induced by the strain, and their spatial organization reveals the superstructure. The second nanocomposite contains 5% of spherical silica with a diameter of 20 nm. Its behavior is drastically different. The silica also forms streams of particles (1-2 mu m long); however, the streams are oriented perpendicular to the elongation direction, and that is hardly compatible with the presence of a microfibrillar structure. We assume that this unexpected orientation is produced by the extended growth of mesophases and crystallites perpendicular to the orientation and that stacked lamellae are formed rather than microfibrils.