Electrochemical cycling of lithium battery cathodes introduces large absolute changes in lithium concentration that can result in microstructural damage and cation disorder. This damage can influence the long-term performance of battery systems, but has not to date been investigated in detail. We have conducted direct observations using transmission electron microscopy (TEM) of electrochemically cycled LixCoO2 and LixAlyCo1-yO2 cathodes. A rich variety of electrochemical cycling-induced damage is found. Intercalation oxide particles show widely varying degrees of damage suggesting differing depths of cycling on a local scale. Many particles exhibit severe strain, high dislocation densities, and localized fracture. Moreover, in particles that are severely strained, electron diffraction reveals two types of cation disorder brought about by electrochemical cycling. One is the Li and Co substitution/vacancies on their respective octahedral layers. The second is an evolution towards spinel ordering that is not detectable by bulk analytical methods such as X-ray diffraction (XRD). Unlike previously described ＇lithiated spinels,＇ the observed spinel ordering is characterized by tetrahedral 8a site occupancy even at compositions near x similar to 1. Thus it is shown that even in LiCoO2, widely considered to be the most stable of the intercalation oxides in the layered alpha-NaFeO2 structure, electrochemical cycling results in a transformation towards spinel cation ordering. Similar results are seen in LixAlyCo1-yO2. Cumulative damage of this kind may contribute to the degradation of LiCoO2 cathodes after long-term cycling.