Phonon density-of-states and related thermodynamic properties of the α-quartz-type and rutile-type germanium dioxide (GeO2) are investigated from density functional perturbation theory. The significant density-of-states at the low frequencies in the α-quartz-type GeO2 are at the origin of (i) its lower internal energy below 250 K, (ii) its smaller free energy, (iii) its higher entropy, (iv) its lower Debye temperature and (v) its larger positive linear thermal expansion, with respect to the rutile-type GeO2.