Abstract Background and purpose Image Guidance of patient set-up for radiotherapy can be achieved by acquiring X-ray volumetric images (XVI) with Elekta Synergy and registering these to the planning CT scan. This enables full 3D registration of structures from similar 3D imaging modalities and offers superior image quality, rotational set-up information and a large field of view. This study uses the head section of the Rando phantom to demonstrate a new paradigm of faster, lower dose XVI that still allows registration to high precision. Materials and methods One high exposure XVI scan and one low exposure XVI scan were performed with a Rando Head Phantom. The second scan was used to simulate ultra low dose, fast acquisition, full and half scans by discarding a large number of projections before reconstruction. Dose measurements were performed using Thermo Luminescent Dosimeters (TLD) and an ion chamber. The reconstructed XVI scans were automatically registered with a helical CT scan of the Rando Head using the volumetric, grey-level, cross-correlation algorithm implemented in the Syntegra software package (Philips Medical Systems). Reproducibility of the registration process was investigated. Results In both XVI scans the body surface, bone-tissue and tissue air interfaces were clearly visible. Although the subjective image quality of the low dose cone beam scan was reduced, registration of both cone beam scans with the planning CT scan agreed within 0.1 mm and 0.1°. Dose to the patient was reduced from 28 mGy to less than 1 mGy and the equivalent scan speed reduced to one minute or less. Conclusions Automatic 3D registration of high speed, ultra low dose XVI scans with the planning CT scan can be used for precision 3D patient set-up verification/image guidance on a daily basis with out loss of accuracy when compared to higher dose XVI scans.