Synchrotron X-ray microtomography has been utilized for the 3D characterisation of microstructure of aluminium foams. A combination of phase contrast imaging technique and several application techniques, such as local area tomography, microstructural gauging and in-situ observation, has enabled the assessment of microstructural effects on compressive deformation behaviours. It has been clarified that ductile buckling of a cell wall occurs regardless of any of the above microstructural factors in the case of a pure aluminium foam, while rather brittle fracture of a cell wall is induced by the existence of coarse micro-pores independently of the intermetallic particles and the grain boundary in the case of Al-Zn-Mg alloy foams. When cooling rate during foaming is high, however, lower energy absorption might be attributable to the significant amount of residual foaming agent particle and its inhomogeneous distribution. These tendencies are also confirmed by 3D strain mapping by tracking internal microstructural features.