A molecular scale and microstructural description of the hydrate phases resulting from the hydration of Portland cement or blends of Portland cement with supplementary cementitious materials is essential for improving and controlling the physical and chemical properties of cement-based materials. The main hydrates are characterised by the absence of long-range order, preventing detailed structural studies by diffraction techniques. This paper illustrates and reviews recent advances in hydrate characterisation by transmission electron microscopy, solid-state nuclear magnetic resonance, and Raman spectroscopy. These techniques are suitable for characterisation of complex mixtures including crystalline as well as amorphous phases and provide important information about the composition and structure on the nano- and microscale.