The first 3-D direct observation of clusters of Nd oxide inside silicate glasses was achieved using atom probe tomography. Three-dimensional elemental maps of major chemical elements in glasses such as Si, Al, Zn and O showed no evidence of regions that had concentrations higher than the average values, whereas the Nd aggregated into regions of high concentration. Elemental maps of Nd and Pb recorded from the glasses containing PbS QDs showed highly-concentrated areas of both elements at the same locations; this result indicates that PbS QDs formation started in association with the Nd clusters.