The properties of the high-temperature superconductor YBa 2 Cu 3 O 7−x (YBCO) depend on the concentration of oxygen vacancies (V O). It is generally agreed upon that V O form in the CuO chains, even at low concentrations where the critical temperature for superconductivity peaks (x ≈ 0.07), with only a handful of reports suggesting the presence of V O at the apical sites. In this paper, we show direct evidence of apical V O in optimally doped YBCO samples. Using density-functional-theory calculations, we predict that isolated V O are equally favorable to form in either the CuO chains or the apical sites, which we confirm using atomic-resolution scanning transmission electron microscope imaging and spectroscopy. We further show that apical V O lead to significant lattice distortions and changes in the electronic structure of YBCO, indicating they should be considered on an equal footing with chain V O to understand the superconducting properties of YBCO in the optimal doping region.