Objective: The aim of this study was to evaluate the correlation between the length of the infundibulum and ostium height with the anatomic variations of osteomeatal complex (OMC) and sinus pathology using cone-beam computed tomography (CBCT). Methods: CBCT images of 204 patients (408 maxillary sinuses) were evaluated retrospectively. The height of the ostium and the length of the infundibulum were measured. The presence of maxillary sinus pathology, nasal septal deviation, Haller cells, concha bullosa, and sinus septa were analyzed. The correlation between the size of the maxillary sinus drainage system and anatomic variations was compared using the t test, Fisher’s exact test, and χ² test. The effect of tooth loss on the length of the infundibulum and ostium height was also analyzed using ANOVA. Results: The height of the ostium and the maximal septal deviation angle were found to be significantly greater in males (p < 0.05). As ostium height increased, the presence of maxillary sinus septa increased (p < 0.05). No statistically significant association was detected between other variations and the length of infundibulum or ostium height. The relationship between tooth loss and both the length of the infundibulum and ostium height were found to be insignificant (p > 0.05). Conclusions: Radiographic examination, especially on CBCT images, is important for an evaluation of maxillary sinuses. here, we demonstrated a significant relationship between ostium height and the presence of maxillary sinus septa. However, it was found that nasal septal deviation, concha bullosa, Haller cells, and other sinusopathies did not have a major effect on the size of the maxillary sinus drainage system.