Poly(ethylene-2,6-naphthalate) (PEN) was crystallized from the glassy state at atmospheric pressure (beyond the end of primary crystallization) and from the melt at high pressure. The structure was characterized using small-angle X-ray scattering (SAXS), wide-angle X-ray scattering (WAXS), differential scanning calorimetry (DSC) and density measurements. The SAXS patterns were analysed using the interface distribution function (IDF) method. For the materials prepared at ambient pressure the crystallinity inside the layer stacks remains nearly constant during the secondary crystallization process. On the other hand, the volume filled with the stacks increases as a function of crystallization temperature (T-c) and time (t(c)). For T-c > 200 degreesC secondary crystallisation goes along with a dynamic rearrangement of the primary stacks, as concluded from variations of the layer thickness distributions in the SAXS data. For T-c < 200 degreesC primary lamellae are stable, and both insertion of new crystal lamellae into existing stacks and generation of additional stacks is found. In contrast to PET, two different kinds of layer stacks are not observed in the PEN nano-composites. Materials prepared at 400 MPa exhibit high roughness of the crystalline domain surfaces. Depending on T-c there is a continuous transformation from the alpha to the beta -crystal modification, but hardly any change of the long period. Crystal thickness increases, both at the expense of the amorphous thickness and of the volume filled with lamellar stacks. The structure of samples showing two melting peaks is discussed in terms of a dual lamellar contribution of correlated and uncorrelated nano-crystallites, respectively.