High-resolution electron microscopy is used to study the initial growth of different REBa2Cu3O7−δ thin films. In DyBa2Cu3O7−δ ultra-thin films, deposited on TiO2 terminated SrTiO3, two different types of interface arrangements occur: bulk–SrO–TiO2–BaO–CuO–BaO–CuO2–Dy–CuO2–BaO–bulk and bulk–SrO–TiO2–BaO–CuO2–Dy–CuO2–BaO–CuO–BaO–bulk. This variable growth sequence is the origin of the presence of antiphase boundaries. In Nd1+xBa2−xCu3O7−δ thin films, antiphase boundaries tend to annihilate by the insertion of extra Nd-layers. This annihilation is correlated with the flat morphology of the film and the absence of growth spirals at the surface of the Nd-rich films.