Different biomaterials have been proposed as scaffolds for the delivery of cells and/or biological molecules to repair or regenerate damaged or diseased bone tissues. Particular attention is being given to porous bioceramics that mimic trabecular bone chemistry and structure. Chemical composition, density, pore shape, pore size, and pore interconnection are elements that have to be considered to improve the efficiency of these biomaterials. Commonly, two-dimensional (2D) systems of analysis such as scanning electron microscope (SEM) are used for the characterization and comparison of the scaffolds. Unfortunately, these systems do not allow a complete investigation of the three-dimensional (3D) spatial structure of the scaffold. In this study, we have considered two different techniques, that is, SEM and 3D synchrotron radiation (SR) micro-CT to extract information on the geometry of two hydroxyapatite (HA) bioceramics with identical chemical composition but different micro-porosity, pore size distribution, and pore interconnection pathway. The two scaffolds were obtained with two different procedures: (a) sponge matrix embedding (scaffold FB), and (b) foaming (scaffold EP). Both scaffolds showed structures suitable for tissue-engineering applications, but scaffold EP appeared superior with regard to interconnection of pores, surface on which the new bone could be deposited, and percentage of volume available to bone deposition.