Microcrystalline silicon and its group IV alloys are widely explored as absorber layers in thin film solar cells. Despite the extended research in recent years the fundamental understanding of the relation between macroscopical properties, i.e. electrical and optical properties, and the microstructure is poor. Clearly, the structure of microcrystalline materials, consisting of a phase mixture between “amorphous” material, crystalline grains, and voids, is complex. To demonstrate the strengths and limitations of transmission electron microscopy on microcrystalline materials, we will discuss different techniques employed to investigate grain sizes and morphologies, crystallographic orientations, amorphous volume fractions, and lateral arrangements of crystallites. In particular, we focus on the potential for analyzing the structure of grain boundaries and the amorphous phase in microcrystalline silicon and silicon carbide by the most advanced techniques in atomic resolution imaging in the transmission electron microscope.