Background: This study assessed the relationship between mucosal thickness (MT) of the maxillary sinus and periodontal bone loss (PBL) and periapical condition of related teeth. We also aimed to identify the association between root apices and the inferior wall of the maxillary sinus using Cone beam computed tomography (CBCT). Material and Methods: In this study, CBCT images of 205 patients with 410 maxillary sinuses were examined, retrospectively. A total of 582 maxillary molars and 587 premolars were observed. The relationship of each root with maxillary sinus and apical lesions of these roots were classified, PBL was examined and the situations of adjacent teeth were estimated. The effect of these conditions on sinus mucosal thickness (MT) was evaluated. Results: There was a significant correlation between MT of maxillary sinus and both PBL and age (r = 0.52, p =0.000 and r = 0.111, p = 0.002, respectively). The frequency of MT increased as the severity of apical lesion enlarged. A positive correlation was found between MT and degree of PBL and periapical lesions. To reveal the association between MT and pulpoperiapical condition bivariate correlation was done and a significant relationship between the pulpoperiapical condition and MT was found (r = 0.17, p =0.000). Conclusions: This retrospective study showed that MT of the maxillary sinus was common among patients with PBL and MT was significantly associated with PBL and apical lesions. The relationship of maxillary sinus to adjacent teeth had also positive correlation with MT. CBCT imaging enabled better evaluation of maxillary sinus, posterior teeth and surrounding structures compared to other imaging tools