<p>Horizontal and vertical position of the maxillary molar roots in relation to the sinus floor was compared between subjects with and without odontogenic related mucosal thickening (MT) using cone-beam computed tomography (CBCT). CBCT images of 330 subjects were evaluated based on the observation of odontogenic related MT. Moreover, horizontal and vertical position of the maxillary molar roots in relation to the sinus floor was investigated and categorized. Pearson Chi-Square and Fisher’s exact tests were used for the statistical comparisons with the significance level set at 0.05. Among the horizontal relationships, “BP” which refers to the lowest point of the sinus floor being positioned between the buccal and palatal roots was the most frequent in the first and second molars. With respect to the vertical relationships, “2b” variant which refers to the root apices being in contact with the sinus floor without its elevation was the most common type. A significant relationship was found between MT and horizontal relation type “B” in the first molars which refers to the lowest point of the sinus floor being positioned on the buccal side of the buccal roots (<i>p</i> = 0.009 and 0.028 on the right and left sides, respectively). Nevertheless, no significant relationship was observed between vertical positions and MT. Odontogenic related MT is more frequently encountered when the maxillary sinus floor is positioned on the buccal aspect of the first molar roots. Hence, surgical and endodontic procedures in the posterior region of the maxilla have to be performed with great caution in buccally positioned sinuses to avoid odontogenic related sinusitis.</p>