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Background The proximity of the maxillary sinus floor to the maxillary molar roots increases the probability of oroantral communication on conducting any surgical or endodontic procedure in the involved area. The aim of this study is to evaluate the relationship between each maxillary molar root and maxillary sinus floor using cone beam computed tomography. Predicting the probability of protrusion of each root into the sinus will consequently predict the probability of occurrence of the oroantral fistula in a sample of the Egyptian population. Results The total number of roots located outside the sinus was 121 (35.3%), while those contacting the sinus floor were 80 (23.3%) and those intruded the sinus were 141 (41.2%). The percentage of root intrusion into the sinus in males (56.9%) was significantly (p = 0.01) higher than females (42.9%). The probability of root intrusion in the left molars (54.2%) was non-significantly (p = 0.067) higher than that of the right side (44.3%). As for the type of tooth, the second molar showed the highest probability of root intrusion into the sinus (55.3%) followed by the third molars (52.6%) then the first molars (40.9). According to the type of root, the mesiobuccal root showed the highest probability of intrusion into the sinus (50.9%) followed by the palatal root (49.1%) then the distobuccal root (47.4%). However, the difference in both type of tooth and type of root was statistically non-significant (p = 0.051 and 0.869 respectively). As for the individual root with the highest probability of intrusion, the mesio-buccal root of the right third molar is the most frequent root to intrude the sinus (71.4%) and the mesio-buccal root of the right first molar is the least frequent (22.7%). Conclusions In a sample of the Egyptian population, males exhibit higher probability of root protrusion into the sinus than females. The side and type of tooth are of higher impact on the probability of its intrusion into the sinus compared to the type of root. Left second molars are at a higher risk of oroantral communications on surgical or endodontic procedures compared to other molars due to its highest probability of intrusion into the sinus.