The high porosity and microstructure of bio-aggregates are fundamental to their physical properties. Typically they have a low density and a complex pore structure. This has two principal effects. In the first instance, low density is associated with low strength, but also with low thermal conductivity. For this reason most bio-aggregates are not suitable for use as structural materials, but are eminently suited to act as a low density filler in composite materials conferring low thermal conductivity on the resulting bio-composite. The complex nature of their porosity results in a material that is able to readily adsorb moisture and humidity. This results in a material that has an exceptionally high moisture buffering capacity, a characteristic that is of great interest in building materials, because it tends to stabilise the internal environment of a building, thereby resulting in a much more healthy indoor environment. This chapter considers the range of methods that can be used to measure porosity and to characterise the microstructure of materials in general, and discusses how some of these techniques have been used on bio-aggregates. It also identifies opportunities to use novel techniques on bio-aggregates in order to improve our understanding of their porosity, pore size distribution, pore connectivity and microstructure, all of which are characteristics that are essential to the optimisation of the performance of bio-aggregates within the construction industry.