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Objective: This study aimed to evaluate the sphenoid sinus septation, the presence/absence of Onodi cells, and the relationship between these structures with each other in cone-beam computed tomography. Methods: A total of 500 cases (250 males, 250 females) between the ages of 18 and 81 were included in this study. Sphenoid sinus septations were classified as intersphenoid, multiple, and absent, and Onodi cells as present or absent. The relationship between these parameters was also assessed. Chi square test was used to determine the relationship between sphenoid sinus septation and Onodi cells. Results: Multiple septa seen in 451 (90.2%) of the cases is the most common type of sphenoid septation. Onodi cells were present in 327 (65.4%) of the cases. A statistically significant relationship was detected between Onodi cells and mean age (P < .05) but no significant difference was observed between the septation and mean age (P > .05). There was no significant difference between the septation or Onodi cells with gender (P > .05). Multiple septa were observed in all cases with Onodi cell. The relationship between sphenoid sinus septation and Onodi cell was statistically significant (P < .001). Conclusion:This study revealed that there was a significant relationship between sphenoid sinus septation and Onodi cells. The presence of Onodi cells was observed only with multiple septa. Cone-beam computed tomography is an effective imaging method in the evaluation of sphenoid sinus anatomy and its variations and surrounding anatomical structures.