Sinus augmentation procedure has been demonstrated to be a highly predictable treatment in posterior maxilla atrophy. All the surgical interventions in the maxillary region require deep knowledge of anatomy and possible anatomical variations. In this article, pre-operative and post-operative assessments of sinus cavity as well as novel approaches to deepen our knowledge of the behavior of bone substitute materials are described. The awareness of the patient's morphologic conditions enables exact planning of invasive surgery and aids to avoid complications. Pre-operative radiologic evaluation of the region before sinus lift is advisable both for a planning of the sinus augmentation and for selection and alignment of the optimum placement of implants. On the orthopantomography it is possible to measure the vertical dimension of graft, but not the volume and 3D changes. Cone-beam computed tomography (CBCT) has become the "gold standard" to plan a comprehensive implant treatment and to achieve a post-operative assessment. A computer-aided design/computer-aided manufacturing (CAD/CAM) technique is proposed to produce custom-made block grafts for sinus lift procedure, and a customized cutting guide to accurately place the lateral wall and ease membrane elevation. This procedure allows to reduce intervention time, to precisely adapt the scaffold, to reduce risk of complications and to improve operation quality. Recently, a novel approach has been used to deepen our knowledge of the behavior of BSBs: by means of synchrotron micro-tomography (SCT). It is a 3-D analyzing method, suitable to examine the dynamic and spatial arrangement of regenerative phenomena in complex anatomical structures such as bone, where tissues with several morphologies (alveolar process, unmineralized extracellular matrix, regenerated vessels, etc.) compete to achieve the final goal of bone regeneration.