The purpose of our study was to compare micromorphometric data obtained by cone-beam computed-tomography (CBCT) and microcomputed-tomography (micro-CT) of the augmented sinus and to evaluate the long-term stability of the bone gain achieved using BoneAlbumin. Sinus lifts, and after 6-months, healing bone-biopsy and implant placement were carried out. Specimens were analyzed by micro-CT. A total of 16 samples were collected from nine patients (mean age 54.7 +/- 6.5 years). Pre-, postoperative, and 3-year control CBCT-data were registered to determine from where the biopsy samples were harvested. Micromorphometric variables were calculated from the micro-CT- and CBCT-data, and their correlation was determined by Spearman's test. The volume of augmented bone was calculated at the time of implant placement and after 3 years. A positive correlation was found between bone-volume fraction, trabecular-separation, open-, and total-porosity, while a negative correlation was found between trabecular-thickness obtained from CBCT- and micro-CT-data (p < 0.05). Mean volumetric reduction of 39.28% (11.88-60.02%) was observed. Correlation of CBCT- and micro-CT-data suggested that micromorphometric analysis of CBCT reconstructions of the augmented sinuses provided reliable information on the microarchitecture of augmented bone. CBCT as a modality might be adequate in the analysis of bone quality in the augmented sinus. At the 3-year, control sinus grafts showed volumetric stability.