The use of cone beam computed tomography (CBCT) in diagnostic radiology departments is increasing. Several discussions arise whether the CBCT application, some multi-slice (MSCT) examinations can be replaced by it. High hopes are set regarding the dosimetric aspects of CBCT: are patient doses in between those from conventional X-rays and MSCT? In this study effective dose and organ doses were evaluated for two non-dental CBCT examinations: sinus and middle ear. A comparison with the dose obtained with MSCT protocol was performed. Moreover, the sinus examination was also compared with the dose obtained by projection radiography (RX). Effective doses were estimated from thermoluminescent detector dose measurements in an anthropomorphic phantom and were compared against Monte Carlo simulations. Results show that the effective dose for the sinus examination is more than three times higher with the MSCT than with CBCT and about five times lower with RX compared with CBCT, whereas for the middle ear examination the effective dose obtained with MSCT is almost six times higher than that of CBCT. Finally, a sensitivity study on the size and position of the CBCT field of view showed the influence of these two factors on the dose received by the patient.