Two very different pulsed laser deposition rates, 192 and 6 Å/s, were used to produce 1 μm thick superconducting YBa2Cu3Ox (YBCO) films on (001) SrTiO3 single-crystal substrates at 790 °C. Transmission electron microscopy (TEM) was used to characterize and compare microstructures between the two films. It has been found that the high deposition rate led to a slight deviation from the expected epitaxial orientations, and extra stress was induced in the films by increased lattice mismatch between the films and the substrates. In addition, misoriented YBCO grains were formed in the high-rate films after a thickness of about 150 nm. Postannealing in oxygen had no visible influence on these defects, although superconducting properties were improved significantly. In contrast to the high-rate films, overall epitaxial orientations have been formed in the low-rate films, and no misoriented YBCO grains were found. However, variations in lattice parameters and columnar voids were observed, although their existence apparently does not have considerable influence on superconducting current density (Jc). Cation disorder was observed in both films. A two-step film growth mechanism is concluded which is responsible for the formation of some defects in the high-deposition rate films.