Copper oxide quantum dots (QDs) were grown in various thicknesses on different SrTiO 3(001) surfaces and were characterized using various surface and bulk sensitive techniques. The experimental growth conditions were optimized to obtain Cu 2O as the major phase in these structures. The copper oxide QDs grown on clean SrTiO 3(001) surfaces at 825 K or higher with p(O 2) of 9.0×10 -7 Torr or above contain mostly Cu(II) in contrast to those grown at 800 K with p(O 2) of ∼7.0×10 -7 Torr that contain primarily Cu(I). Furthermore, it has been established that there is a strong interaction between the SrTiO 3(001) surface and the first few monolayers of these nano structures, which induces the formation of Cu(II). However, this interaction is mitigated with increasing thickness of copper oxide QDs resulting in the exclusive formation of Cu 2O in the topmost layers. Modification of substrate surfaces using chemical treatment and/or energetic Au 2+ ion-beam irradiation affects the formation of these structures.