The vacancy ordering behavior of an A-site deficient perovskite system, Ca1–xLa2x/3TiO3, was studied using atomic resolution scanning transmission electron microscopy (STEM) in conjunction with electron energy-loss spectroscopy (EELS), with the aim of determining the role of A-site composition changes. At low La content (x = 0.2), adopting Pbnm symmetry, there was no indication of long-range ordering. Domains, with clear boundaries, were observed in bright-field (BF) imaging, but were not immediately visible in the corresponding high-angle annular dark-field (HAADF) image. These boundaries, with the aid of displacement maps from A-site cations in the HAADF signal, are shown to be tilt boundaries. At the La-rich end of the composition (x = 0.9), adopting Cmmm symmetry, long-range ordering of vacancies and La3+ ions was observed, with alternating La-rich and La-poor layers on (001)p planes, creating a double perovskite lattice along the c axis. These highly ordered domains can be found isolated within a random distribution of vacancies/La3+, or within a large population, encompassing a large volume. In regions with a high number density of double perovskite domains, these highly ordered domains were separated by twin boundaries, with 90° or 180° lattice rotations across boundaries. The occurrence and characteristics of these ordered structures are discussed and compared with similar perovskite systems.