This study aimed to develop geometry of irradiation applicable to the software PCXMC for organs dose estimate and the consequent calculation of effective dose in applications of Cone Beam Computed Tomography (CBCT). Three different CBCT scanners for dental applications were evaluated: CareStream CS 9000 3D; i-CAT, and Gendex GXCB-500. Initially, each image protocol was characterized dosimetrically, measuring the incident air kerma, K i and the product of air kerma-area product, P KA . A Radcal solid state detector and a PTW transmission chamber were used for this purpose. Then the technical parameters, dosimetric parameters, and geometric conditions of each preset protocol were input in the PCXMC™ software to calculate the values of effective dose. The dose values in organs and tissues vary according to the protocol used and the centering of the x-ray beam. The calculated effective dose was within the range of (15.7 to 18.7 μSv)/(41.9 to 55.7 μSv) for CS 9000 3D, (70.6 to 72.6 μSv)/(76.6 to 83.2 μSv) for the GXCB-500, and (85.9 to 120 μSv)/(114.0 to 141.1 μSv) for the Classical i-CAT. These values were compared with results obtained from dosimetric data using a thermoluminescent dosimeter, TLD, implanted in an anthropomorphic phantom. The comparison between the values obtained by PCXMC and TLD data was considered consistent. The effective dose results were very sensitive to the geometry of radiation (beam position in the mathematical stylized phantom). This factor indicated the limitations of the software used. However, the software used is very useful as a tool in the optimization process for image protocols and the awareness of professionals. It can be concluded that the use of the PCXMC Monte Carlo simulation software was useful for the assessment protocols for CBCT dental applications.