Many of the remarkable electrical and optical properties of organic semiconductors are governed by the interaction of electronic excitations with intra- and intermolecular vibrational modes. However, in specific systems this interaction is not understood in detail at a molecular level and this has been due, at least in part, to the lack of easy-to-use and widely available experimental probes of the structural dynamics. Here we demonstrate that thermal diffuse scattering in electron diffraction patterns from organic semiconductors, such as 6,13-bistriisopropyl-silylethynyl pentacene, allows the dominant lattice vibrational modes to be probed directly. The amplitude and direction of the dominant molecular motions were determined by comparison of the diffuse scattering with simulations and molecular dynamics calculations. Our widely applicable approach enables a much deeper understanding of the structural dynamics in a broad range of organic semiconductors.