Back pain constitutes a major problem in modern societies. Facet joints are increasingly recognised as a source of such pain. Knowledge about the internal morphology and its changes with age may make it possible to include the facets more in therapeutic strategies, for instance joint replacements or immobilisation. In total, 168 facets from C6/7 and L4/5 segments were scanned in a micro-computed tomography. Image analysis was used to investigate the internal morphology with regard to donor age and gender. Additional data from trabecular bone of the vertebral core allowed a semi-quantitative comparison of the morphology of the vertebral core and the facets. Porosity and pore spacing of the cortical sub-chondral bone does not appear to change with age for either males or females. In contrast, bone volume fraction decreases in females from approximately 0.4 to 0.2, whereas it is constant in males. Trabecular thickness decreases during the ageing process in females and stays constant in males, whereas trabecular separation increases during the ageing process in both genders. The results of this study may help to improve the understanding of pathophysiological changes in the facet joints. Such results could be of value for understanding back pain and its treatment.