Variable-angle high-angle annular dark-field (HAADF) imaging in scanning transmission electron microscopy is developed for precise and accurate determination of three-dimensional (3D) dopant atom configurations. Gd-doped SrTiO3 films containing Sr columns containing zero, one, or two Gd dopant atoms are imaged in HAADF mode using two different collection angles. Variable-angle HAADF significantly increases both the precision and accuracy of 3D dopant profiling. Using image simulations, it is shown that the combined information from the two detectors reduces the uncertainty in the dopant depth position measurement and can uniquely identify certain atomic configurations that are indistinguishable with a single detector setting. Additional advances and applications are discussed.