Purpose: This study evaluated the distance from the posterior root apices to the maxillary sinus floor (MSF) and the frequency of roots touching or protruding through the MSF using cone-beam computed tomography (CBCT). Materials and Methods: This study included 100 subjects divided into different vertical and anteroposterior skeletal growth patterns. On CBCT images, the distance from the posterior root apices to MSF was measured and the frequency of roots touching or protruding through the MSF was evaluated using NNT software (version 5.3.0.0; ImageWorks, Elmsford, NY, USA). Results: No statistically significant differences were found in the distance from the posterior root apices to the MSF among vertical skeletal groups (P>0.05). The palatal roots of the first molar and the palatal, mesio-buccal and disto-buccal roots of the second molars had significantly less distance from MSF in skeletal class II than in class III (P<0.05). The high-angle group had the highest frequencies of roots touching or protruding into the maxillary sinus (49.8%); the lowest proportion of these roots was found in skeletal class III (28.3%) and the highest proportion in class II (50.3%). Males had shorter distances from the posterior root apices to the MSF and higher frequencies of roots protruding through or touching the MSF than females. Conclusion Anteroposterior skeletal growth patterns and sex affected the distances from the maxillary posterior roots to the MSF. The frequency of roots protruding into or touching the sinus was affected by both vertical and anteroposterior skeletal groups and sex. These findings have implications for dental practice.