Ge nanocrystals (NCs) in GeO2 films obtained with the use of two methods were studied. The first method is a film deposition from supersaturated GeO vapor with subsequent dissociation of metastable GeO on heterophase system Ge:GeO2. The second method is growth of anomalous thick native germanium oxide layers with chemical composition GeOx(H2O) during catalytically enhanced Ge oxidation. The obtained films were studied with the use of photoluminescence (PL), Raman scattering spectroscopy, high-resolution electron microscopy (HREM). Strong PL signals were detected in GeO2 films with Ge-NCs at room temperature. “Blue-shift” of PL maximum was observed with reducing of Ge excess in anomalous thick native germanium oxide films. Also a correlation between reducing of the NC sizes (estimated from position of Raman peaks) and PL “blue-shift” was observed. The Ge NCs presence was confirmed by HREM data. The optical gap in Ge-NCs was calculated with taking into account quantum size effects and compared with the position of the experimental PL peaks. It can be concluded that a Ge-NC in GeO2 matrix is a quantum dot of type I.