We report on three-dimensional (3D) imaging of individual Gd dopant atoms in a thin (∼2.3 nm) foil of SrTiO3, using quantitative scanning transmission electron microscopy. Uncertainties in the depth positions of individual dopants are less than 1 unit cell. The overall dopant concentration measured from atom column intensities agrees quantitatively with electrical measurements. The method is applied to analyze the 3D arrangement of dopants within small clusters containing 4-5 Gd atoms.