Tissue development in multicellular animals relies on the ability of cells to synthesise an extracellular matrix (ECM) containing spatially-organised fibrous assemblies, the most widespread of which is based on collagen fibrils whose length greatly exceeds that of individual cells. The importance of the correct regulation of fibril deposition is exemplified in diseases such as osteogenesis imperfecta (caused by mutations in collagen genes), fibrosis (caused by ectopic accumulation of collagen) and cardiovascular disease (which involves cells and macromolecules binding to collagen in the vessel wall). Much is known about the molecular biology of collagens but less is known about collagen fibril structure and how the fibrils are formed (fibrillogenesis). This is explained in part by the fact that the fibrils are non-crystalline, extensively cross-linked, and very large, which makes them refractory to study by conventional biochemical and high-resolution structure-determination techniques. Electron microscopy has become established as the method of choice for studying collagen fibril structure and assembly, and this article describes the electron microscope methods most often used.