The structural changes occurring along the necked region developed when amorphous poly(ethylene naphthalate) (PEN) films are cold drawn were investigated by means of X-ray microdiffraction using synchrotron radiation. The wide-angle X-ray scattering (WAXS) results reveal the appearance of smectic order with a period of 1.25 nm corresponding to a chain repeat length associated with a sinusoidal conformation of the polymer chains (beta-conformation), 5% shorter than that repeat length consisting in molecular chains showing the more extended a-conformation. The smectic order gradually decreases with increasing the distance from the tip of the necked region, showing a discontinuity, which corresponds to the transition zone between the necked region and the bulk, where molecular order suddenly drops. The small-angle X-ray scattering (SAXS) measurements give no indication that the mesophase is associated with a particular microstructure; however, the SAXS equatorial maximum presented at specific positions of the necked region may be related to the formation of small amount of crazelike structures produced by the intersections of shear bands, with shear banding and shear yielding being the mean deformation behavior as it is supported by scanning electron microscopy (SEM) micrographs. The necked zone induced by cold drawing partially disappears although not completely after annealing, and the residual chain orientation suggests that either the annealing conditions selected were not enough for a full recovery or that a material fraction has undergone plastic deformation.