Purpose This paper presents the development of a protocol for quality control of a megavoltage cone beam CT imaging system (MVCB) mounted on a Siemens Oncor 6 MV linear accelerator. Materials and methods Several parameters were controlled on the MVCB system: (1) the initial geometric calibration of the system; (2) the quality of the images (geometric distortion, uniformity, spatial resolution, low contrast resolution) for various protocols; (3) the correspondence between the intensity of voxels and electronic densities; (4) the dose delivered when achieving a MVCB. These tests were done mainly with two cylindrical phantoms specific to the quality control (QC) of a MVCB system, supplied by Siemens, and with the Catphan 600 phantom (The Phantom Laboratory) and Quasar™ Multipurpose Body phantom (Modus Medical Devices Inc). Results The results of the quality control of the images were within the tolerances. The use of the Catphan 600 phantom was inadequate for the QC of MVCB images. These tests also highlighted the need to correct the MVCB images for the “cupping artefact” for dose calculation purpose. Conclusion The initial characteristics of the MVCB imaging system were established. Such testing also provided the assessment of the influence of various parameters on the image quality as well as the associated dose delivered during their acquisition, and emphasized the corrections needed to use MVCB images for dose calculation.