The defect responsible for the transparent to red color change of nominally undoped ZnO bulk single crystals is investigated. Upon annealing in the presence of metallic Zn as reported by Halliburton et al. and also Ti and Zr a native defect forms with an energy level about 0.7 eV below the conduction band. This change is reversible upon annealing in oxygen. Optical transmission data along with positron depth profiles and annealing studies are combined to identify the defect as oxygen vacancies. Vacancy clustering occurs at about 500 °C if isolated zinc and oxygen vacancies. In the absence of zinc vacancies, clusters form at about 800 °C.