Introduction: The proximity of the roots to the maxillary sinus can create a variety of risks. Objective: To evaluate the relationship between the roots of healthy teeth and the maxillary sinus, as well as the occurrence of sinus pathologies. Methods: Three radiologists analyzed 109 cone beam computed tomography (CBCT) images. The Kappa test was used to assess the intra- and inter-rater agreement. The chi-squared test and prevalence ratio were used to test the hypothesis that roots of healthy teeth in the maxillary sinus favored the occurrence of sinus pathologies (p = 0.01). Results: Intra- and inter-rater agreement ranged from good to excellent. The chi-squared test demonstrated a statistically significant difference (p = 0.006) between the tooth roots in diseased maxillary sinuses (6.09%) and those in normal sinuses (3.43%). The prevalence ratio test showed a statistically significant higher prevalence of tooth roots in diseased sinuses than in normal sinuses (p < 0.0001). Roots in the maxillary sinus were 1.82 times more associated with diseased sinuses. Conclusion: Dental roots in the maxillary sinus are almost twice as likely to be associated with diseased sinuses than normal sinuses. Healthy teeth whose roots are inside the maxillary sinus may induce an inflammatory response in the sinus membrane. It is suspected that dental procedures may exacerbate the condition.