Aim: To compare the qualitative and quantitative information yielded by imaging modalities on the evaluation of the relationship between the maxillary sinus and the apices of posterior teeth. Methods: Three oral radiologists examined 109 panoramic radiographs and cone-beam computed tomography (CBCT) images obtained from a digital archive. A total of 1,875 apices were classified according to their topographic relationship in both imaging modalities. Agreements between the two imaging techniques were examined statistically. The evaluation was repeated in 25% of the sample to statistically evaluate the intraobserver agreement, with a 30-day interval. Results: The values found in the Kappa test for qualitative assessment and the intraclass correlation coefficient (ICC) for quantitative assessment showed nearly perfect and excellent correlation, respectively. Regarding the correlation between the two images, the Kappa test in the quality assessment showed a slight correlation between the palatal roots of the right first molars and second molars. Moreover, the quantitative evaluation by ICC showed poor agreement for the palatal roots of the left first molar and second molar, as well as for the buccomesial of the right second molars and for the buccodistal of the left second molars. Conclusions: There is low correlation between panoramic radiography and CBCT when roots are in contact or above the maxillary sinus floor. A high level of agreement was observed when roots are below the maxillary sinus floor.