Objectives: Mucous retention cyst (MRC) is a benign and self-limited lesion that can be caused by many risk factors, including anatomical variations of the sinonasal region. This study aims to investigate the relationship between anatomical variations and the presence of MRC. Materials and Methods: In total, 2109 sinonasal cone beam computed tomography images were evaluated for the presence of MRC, and the sinonasal anatomical regions such as the osteomeatal complex (OMC), infundibulum length, ostium height, the diameter of the ostium, the presence of accessory ostium, concha bullosa, and mucosal thickening of the maxillary sinuses. Shapiro-Wilk normality test, independent sample t-test, and chi-square test were used for statistical analysis, and P < .05 was considered significant. Results: The prevalence of MRC was 119 (5.6%) cases. The average diameter of the ostium in cases with and without MRC was 0.49 ± 0.41 mm and 0.99 ± 0.76 mm, respectively, which showed a significant inverse relationship( P < .001). A significant relationship was found between the septum deviation, the ostium height, the concha bullosa, and the accessory ostium with the presence of MRC ( P < .001). Conclusions: Sinonasal anatomical variations such as ostium diameter, ostium height, septal deviation, the presence of accessory ostium, and concha bullosa can cause MRC development, and considering that surgery may be necessary in some cases; this could be of great importance to clinicians and surgeons for treatment and prevention of development or recurrence of these pseudocysts in patients.