A comparative study of free charge relaxation in amorphous and partially crystallized poly(ethylene-2,6-naphthalene dicarboxylate) (PEN) and poly(ethylene terephthalate) (PET) has been carried out by thermally stimulated depolarization currents (TSDC), differential scanning calorimetry (DSC), and X-ray diffraction. Amorphous films have been crystallized thermally at temperatures between 170 and 200 degrees C (PEN); 100 and 150 degrees C (PET) by the thermal stimulation by steps method. The windowing polarization (WP) technique has been applied to form PET and PEN thermoelectrets. TSDC of these electrets polarized at 86 degrees C (PET) and 130 degrees C (PEN) show only one peak which is attributed to space charge relaxation (p peak). The evolution of this peak has been fitted to the general kinetic order model. DSC measurements of these samples show the appearance of a small endothermic prefusion peak once the crystallization of the sample is completed. This peak increases and shifts towards higher temperatures as the sample is further thermally treated. Associated with the appearance of this endothermic peak, the p relaxation passes through a maximum with a sharp decrease with further heat temperature. The X-ray diffraction measurements of these samples show that the decrease in the p peak is associated with the improvement of the amorphous-crystal interphases.