Aim: To investigate the relationship of maxillary posterior teeth to maxillary sinus in different facial biotypes by using cone-beam computed tomography (CBCT). Materials and methods: In this cross-sectional study, 99 subjects were divided into three facial biotypes—leptoprosopic (LP), mesoprosopic, and euryprosopic facial types. From CBCT images, distances from maxillary posterior roots apices to the sinus floor maxillary posterior roots apices to sinus distance (MSD) were measured and the relationship of each root to maxillary sinus was evaluated using New Net Technologies (NNT) software. Results: Altogether, 1,584 roots of 99 subjects with a mean age of 26.45 ± 6.78 years met the inclusion criteria. Mesoprosopic facial biotypes have significantly lesser MSD than euryprosopic facial types for palatal (P) root of first molar, mesiobuccal (MB), and distobuccal (DB) root of second molar (p < 0.05). Similarly, the LP facial biotypes have significantly lesser MSD than euryprosopic facial biotype for the P root of the first molar and DB root of the second molar (p < 0.05). The mesoprosopic facial biotype has the highest frequency of roots that touch or protrude the sinus (58.1%), followed by LP (45.5%) and euryprosopic (40.1%) facial biotypes. Males have significantly lesser MSD than females for the P root of the first molar, P root of the second molar, and MB root of the second molar (p < 0.05) and have a higher frequency of roots that protrude or touch the sinus (males, 52.5%; females 38.8%). Conclusion: The MSDs and frequency of roots touching or protruding the maxillary sinus vary with different facial biotypes. Mesoprosopic facial biotypes and males tend to have the least MSD and the highest frequency of roots that touch or protrude the maxillary sinus floor (MSF). Clinical significance: These inferences have several implications in dentistry, including root canal therapy, endodontic surgeries, oral surgery, and orthodontics tooth movement and placement of miniscrews.