The microstructure of ion‐implanted thin films of the superconductor YBa2Cu3Ox has been investigated by transmission electron microscopy. The superconducting properties of the films were dominated by large pancake‐shaped grains of YBa2Cu3Ox with their c axis perpendicular to the substrate. Other grains of YBa2Cu3Ox whose c axis was parallel to the substrate formed spherulites. Irradiation with 500 keV O+ ions caused amorphous zones to appear on the grain boundaries between the pancake grains, which initially were free of amorphous or second phases. At higher dose a continuous amorphous layer 150 Å thick was formed. However, the interior of the grains showed no irradiation‐induced microstructural features until they became amorphous at a dose of 3×1014 ions/cm2. The appearance of the amorphous layer on the grain boundaries at low doses accounts for the reduction in the superconducting transition temperature observed in these films.