Dental computed tomography (CT) typically uses a cone-beam geometry with a flat-panel detector. Although the flat-panel detector normally covers the maxillary and mandibular jaws, the cone-beam scan can deliver the dose to organs that are located out of the direct beam path but sensitive to radiation damage, such as eye lens. For typical dentoalveolar cone-beam CT (CBCT) scans, this study investigates the absorbed dose distributions in the head and neck using the Monte Carlo technique, and quantifies specific organ doses. Then, we design an intensity-modulated CBCT scan protocol that can provide a higher tomographic image quality at a lesser patient dose. The beam-intensity modulation includes the changes of tube current (mA) and/or voltage (kVp) during circular scanning, and the modulation scenarios are designed considering the cervical spine through which x-ray beam attenuates largely. We assess the noise-to-dose performances for various intensity-modulation scenarios, and compare the results with that obtained for the conventional scan.