AbstractWe present a study of the structure and chemical composition of the Cr-doped 3D topological insulator Bi₂Se₃. Single-crystalline thin films were grown by molecular beam epitaxy on Al₂O₃ (0001), and their structural and chemical properties determined on an atomic level by aberration-corrected scanning transmission electron microscopy and electron energy loss spectroscopy. A regular quintuple layer stacking of the Bi₂Se₃ film is found, with the exception of the first several atomic layers in the initial growth. The spectroscopy data gives direct evidence that Cr is preferentially substituting for Bi in the Bi₂Se₃ host. We also show that Cr has a tendency to segregate at internal grain boundaries of the Bi₂Se₃ film.