The influence of the characteristic nanostructure of semicrystalline polymers on the segmental dynamics has been studied by dielectric spectroscopy (DS) in poly(ethylene naphthalene-2,6 dicarboxylate) (PEN) samples with different degree of crystallinity. In the investigated temperature range (from -100 to +200 degreesC), three processes have been identified as maxima in the imaginary part of the complex dielectric permittivity (epsilon*). The shape of the alpha -relaxation has been analyzed on the basis of the Havriliak-Negami formalism. Two different levels of restrictions have been found for low and high crystallinity samples. Results from DS and from differential scanning calorimetry (DSC) indicate that the amount of material involved in the alpha process is smaller than the one calculated on the basis of crystallinity. Both effects further support the existence in semicrystalline polymers of an heterogeneous amorphous phase with regions of different levels of mobility.