Detailed microstructure analysis of epitaxial thin films is a vital step towards understanding essential structure-property relationships. Here, a combination of transmission electron microscopy (TEM) techniques is utilized to determine in detail the microstructure of epitaxial La-doped BaSnO3 films grown on two different perovskite substrates: LaAlO3 and PrScO3. These BaSnO3 films are of high current interest due to outstanding electron mobility at ambient. The rotational disorder of low-angle grain boundaries, namely the in-plane twist and out-of-plane tilt, is visualized by conventional TEM under a two-beam condition, and the degree of twists in grains of such films is quantified by selected-area electron diffraction. The investigation of the atomic arrangement near the film-substrate interfaces, using high-resolution annular dark-field scanning TEM imaging, reveals that edge dislocations with a Burgers vector along [001] result in the out-of-plane tilt. It is shown that such TEM-based analyses provide detailed information about the microstructure of the films, which, when combined with complimentary high-resolution X-ray diffraction, yields a complete structural characterization of the films. In particular, stark differences in out-of-plane tilt on the two substrates are shown to result from differences in misfit dislocation densities at the interface, explaining a puzzling observation from X-ray diffraction.