Structural transformations in Ge2Sb2Te5 thin films fabricated by the thermal evaporation in vacuum (TEV) and DC magnetron sputtering (MS) were studied by the differential scanning calorimetry (DSC). Multiple DSC measurements revealed the appearance of reproducible endothermic peaks in all samples in the temperature range of 390–425 °C (one for TEV and two for MS films, respectively). Investigations by X-ray diffraction, scanning and transmission electron microscopes were carried out, and the natures of these endothermic peaks were discussed.