The analysis by microscopy of the compositions and microstructures of geomaterials found in historic structures and buildings is integral to archaeological, art-historical, conservation and restoration-related investigations, and supports decision making for material replacement and repair. In archaeology there is a need to elucidate past social, economic and technological processes, and to understand the environmental impacts of past human activities related to materials use. Standard light and electron microscopy are most commonly employed, but high resolution methods such as transmission electron and three-dimensional tomography such as µ-CT are also being used. Experimental and novel developments, where they overlap with advanced materials science, are uncommon. The application of scientific characterisation frames cultural heritage value, reinforcing our understanding of authenticity and integrity. Characterisation is constrained, in turn, by the values system that operates in cultural heritage. International charters and conservation philosophy necessitate the application of science to contextualising conservation. However, the appearance of science in heritage work has also led to the performance of science for its own sake ('endoscience', sensu Muñoz Viñas, Contemporary Theory of Conservation, Routledge, 2011). This moves some to suggest that there is a disconnect between scientific work and its practical value. Apparent communication problems between scientists applying microscopy and other stakeholders require changes to management of material characterisation in heritage projects.