Cation-deficient perovskites exhibit complex local atomic arrangements which cannot be adequately described by average crystal structure models. By combining reciprocal-space electron diffraction analysis and direct observations of atom positions using state-of-the-art scanning transmission electron microscopy, we clarify the nature of the cation ordering within A-site-deficient perovskite single crystals of La (1Àx)/3 Li x NbO 3 (x ¼ 0 and x ¼ 0.04). Both materials are found to have complex modulated crystal structures with two types of A-cation ordering, namely a long-range layer ordering in alternate (001) p planes and a short-range (intra-domain) columnar ordering within La-rich (001) p layers. The columnar ordering (occupational modulation) produces modulated displacements of Nb and O atoms. It is also found that substitution of even a small amount of Li for La can affect significantly the columnar ordering, leading to a series of structural and microstructural changes that are likely to have a deleterious effect on the Li-ion conductivity of this material.