Structural disorder in molecular crystals is a fundamental limitation for achieving high charge carrier mobilities. Quantifying and uncovering the mechanistic origins of disorder are, however, extremely challenging. Here we use variable coherence transmission electron microscopy to analyze disorder in tri-isopropyl silane pentacene films, utilizing diffuse scattering that is present both as linear streaks and as a slowly varying, isotropic background. The former is due to thermal vibration of the pentacene molecules along their long axis, while the latter is due to static defects kinetically frozen during film deposition. The thermal vibrational amplitude is ∼0.4 Å, while the static displacement parameter in our simplified analysis is much larger (1.0 Å), because it represents the cumulative scattering of all defect configurations that are frozen in the film. Thin film fabrication therefore has an important effect on crystallinity; our technique can be readily used to compare samples prepared under different conditions.