Background: Understanding the morphological characteristics between the floor of the maxillary sinus and the tips of the maxillary posterior roots is crucial in orthodontics involving diagnosis and treatment planning. The aim of this study was to evaluate the distances from the maxillary posterior root apices to the inferior wall of the maxillary sinus, thickness and density of maxillary sinus floor using cone-beam computed tomography images and the relationships between roots and maxillary sinus according to side, and gender. Materials and methods: Three-dimensional images of each root were checked, and the distances were measured along the true vertical axis from the apex of the root to the sinus floor, and the thickness and density of maxillary sinus floor in 60 patients (30 males, 30 female) aged 18 to 25 years. Results: The results showed that the frequency of root contact with the sinus floor increased from 42.5% at the second premolar to more than 91% at the mesiobuccal roots of the second molars. The more protruded root into the sinus floor was the mesiobuccal root apices of the second molars. The distances of both mesiobuccal and palatal roots of second molars and density of second premolar and first molar in left side were significantly higher than the right side, while the thickness of mesiobuccal roots of the second molar was higher in right side than in left side. The distance and density had no significant difference in both males and females, while the thickness of distobuccal and palatal roots of the second molar is higher in females than in males. Conclusion: In conclusion intrusion of the maxillary molars in small distances between root tips and sinus floor could be difficult and slow due to the pneumatization of the maxillary sinus.