The design and improvement of the cathode materials for Li-ion batteries requires the detailed knowledge on the crystal structure at different charge/discharge states and comprehensive understanding of the processes occurring at the nanoscale or even atomic scale level, as many electrode materials demonstrate highly inhomogeneous non-equilibrium behavior. Advanced transmission electron microscopy (TEM) is by far the most suitable and direct tool to view materials down to atomic scale. Recent progress in the electron diffraction methods, related to implication of quantitative electron diffraction tomography, and in the aberration-corrected scanning TEM imaging will be illustrated here with the examples of atomic structure investigation of various cathode materials. Precession electron diffraction and electron diffraction tomography provide quantitative diffraction data with substantially suppressed dynamical effects, enabling reliable structure solution and refinement. In contrast to X-ray and neutron diffraction, the electron diffraction experiments require extremely small quantity of material, which is typically less than 1 mm3, making this method applicable to virtually all samples extracted from electrochemical cells. Electron diffraction patterns can be taken at a very low incoming electron dose, enabling investigation of the materials sensitive to the electron beam irradiation damage, such as polyanion and mixed-anion Li-ion battery cathodes, particularly in their charged state. The capability of quantitative electron diffraction in ab initio structure solution, locating Li atoms and refining the occupancy of the Li positions will be demonstrated using the Li2CoPO4F, Li2FePO4F and LiMn0.5Fe0.5PO4 cathode materials [1]. Aberration-corrected scanning transmission electron microscopy (STEM) techniques deliver the information on the local structural state with sub-angstrom resolution. High angle annular dark field STEM (HAADF-STEM) imaging provides clear visualization of the cation positions, whereas annular bright field STEM (ABF-STEM) shows the location of the “light” elements, such as O and Li. HAADF-STEM method has been applied to investigate the capacity and voltage fading in the layered rock-salt type oxides, which are determined to large degree by the cumulative local structure changes upon continuous electrochemical cycling. A comparative HAADF-STEM study of the layered oxides in the Li-Ru-Ti-O and Li-Ru-Sn-O systems at different stages (pristine, fully charged, discharged and cycled over different number of times) allowed establishing the cation migration pathways during charge-discharge processes and identifying the cation traps responsible for the degradation of the electrochemical performance [2]. Clear visualization of the structure modifications in the oxygen sublattice upon Li extraction is delivered by the ABF-STEM method enabling direct observation of O-O peroxo dimers in Li0.5IrO3 and O vacancy formation in LixFe0.56TeO6 [3,4] and helping to establish the fundamental relation between the anionic redox process and the evolution of the O-O bonding in layered oxides. The figure shows [001] HAADF-STEM and ABF-STEM images of Li0.5IrO3 and the enlarged ABF-STEM image demonstrating the alternating O-O pairs with long and short (marked with dumbbells) projected distances. These O-O dimers arise from twisting the opposite triangular faces of the IrO6 octahedra (shown in yellow). 1. J.Hadermann, A.M.Abakumov, S.Turner, Z.Hafideddine, N.R.Khasanova, E.V.Antipov, G.Van Tendeloo, Chem. Mater., 23, 3540 (2011). 2. M.Sathiya, A.M.Abakumov, D.Foix, G.Rousse, K.Ramesha, M.Saubanère, M.L.Doublet, H.Vezin, C.P.Laisa, A.S.Prakash, D.Gonbeau, G.Van Tendeloo, J-M. Tarascon, Nature Mater., 14, 230 (2015). 3. E.McCalla, A.S.Prakash, E.Berg, M.Saubanere, A.M.Abakumov, D.Foix, B.Klobes, M.-T.Sougrati, G.Rousse, F.Lepoivre, S.Mariyappan, M.-L.Doublet, D.Gonbeau, P.Novak, G.Van Tendeloo, R.P.Hermann, J.-M.Tarascon, J. Electrochem. Soc., 162, A1341 (2015). 4. E.McCalla, A.M.Abakumov, M.Saubanère, D.Foix, E.J.Berg, G.Rousse, M.-L.Doublet, D.Gonbeau, P.Novák, G.Van Tendeloo, R.Dominko, J.-M.Tarascon, Science, 350, 1516 (2015). Figure 1