Megavoltage cone-beam computed tomography (MVCBCT) imaging systems are now available for image-guided radiation therapy delivery and verification. In order to use the three-dimensional anatomical information for dose calculation, the MVCBCT image must provide accurate electron density. This work proposes a new method that has been developed to correct for the cupping and missing data artifacts seen on MVCBCT images of the head and neck region. It uses a conventional kilovoltage CT (kVCT) image as a reference for electron density and rigid registration with a MVCBCT image to obtain correction factors. Dose calculations performed on MVCBCT images corrected with the proposed method agree with calculations done on kVCT images within +/- 1% on phantoms. With patients images the agreement is within +/- 13% above the shoulders and +/- 5% below the shoulder line. This level of dose calculation accuracy allows the use of MVCBCT images for dose verification purposes.