Purpose: The aim of this study was to evaluate the volumetric characteristics of mucous retention cysts (MRCs) in the maxillary sinus and to analyze potential associations of MRCs with dentoalveolar pathologies. Materials and Methods: Cone-beam computed tomography (CBCT) scans exhibiting bilateral maxillary sinuses that were acquired from January 2016 to February 2019 were initially screened. A total of 227 scans (454 sinuses) that fulfilled the inclusion criteria were included. The presence, location, and volumetric characteristics of the diagnosed MRCs were evaluated on CBCT images using the 3D-Slicer software platform. The presence of MRCs was correlated with potential influencing factors including age, sex, and dentoalveolar pathology. For MRCs located on the sinus floor, factors with a potential impact on the volume, surface, and diameter were analyzed. Results: An MRC was present in 130 (28.6%) of the 454 sinuses. Most MRCs were located on the sinus walls and floor. The mean MRC volume, surface, and diameter were 551.21±1368.04 mm3, 228.09±437.56 mm2, and 9.63±5.40 mm, respectively. Significantly more sinuses with associated endodontically treated teeth/periapical lesions were diagnosed with an MRC located on the sinus floor. For MRCs located on the sinus floor, endodontic status exhibited a significant association with increased volume, surface, and diameter. Conclusion Periapical lesions might be a contributing factor associated with the presence and volume of MRCs located on the sinus floor. The 3D-Slicer software platform was found to be a useful tool for clinicians to analyze the size of MRCs before surgical interventions such as sinus floor elevation procedures.