Neutral oxygen vacancies in amorphous (a-) SiO2 and GeO2 as well as bulk a-SiO2 and a-GeO2 configurations have been investigated by using the first-principles pseudopotential method in order to elucidate the mechanism of the photorefractive effect of Ge-doped SiO2. Amorphous configurations of SiO2 and GeO2 have been constructed by quenching using classical molecular-dynamics method and subsequent relaxation using the first-principles method. Obtained configurations and electronic properties are in good agreement with experiments of a-SiO2 and a-GeO2, and the gross features of the densities of states(DOS's)of these glasses are similar to each other. The highest valence band is the O-2p nonbonding band and the lowest conduction band consists of Si or Ge orbitals. However, the structural differences between the a-SiO2 and a-GeO2 configurations such as the larger O-O distance in a-GeO2 and the relatively shorter Ge-Ge distance in a-GeO2 induce the peculiar differences in the DOS's. And the band gap of a-GeO2 is much smaller than that of a-SiO2. The oxygen deficient centers (ODC's) are formed by removing identical oxygen atoms from the Si-O-Si and Ge-O-Ge networks. One occupied defect state is generated in the band gap. The Ge-Ge bond at the Ge-ODC is shorter than the Si-Si bond at the Si-ODC in the present configurations. The larger network flexibility and theless electrostatic repulsion in a-GeO2 than in a-SiO2 should cause the shorter Ge-Ge bond length at the Ge-ODC, which results in the lower occupied defect level in the gap in a-GeO2 and the much lower ODC formation energy in a-GeO2. This smaller formation energy indicates much more ODC's in a-GeO2 than in a-SiO2. Therefore more E8 centers may be generated in Ge-doped a-SiO2 than in pure a-SiO2 if a-GeO2 clusters exist in Ge-doped a-SiO2. Furthermore, we have discussed the electron trapping defects.