High-quality radiotherapy depends upon accurate definition of both disease and normal healthy tissue, and it therefore depends upon high-quality imaging. Image registration is a process that geometrically links two images together and in so doing aligns the anatomical and biological information in these images. Image registration tools are used to incorporate information from other imaging modalities such as MRI, and PET/CT into the radiotherapy planning process, and are now widely used for radiotherapy planning in most tumour sites. Because image registration is a crucial step in the radiotherapy workflow, it is important to understand the limitations of the process, how to assess the quality of an image registration, and to communicate well within teams. Powerful deformable image registration tools are increasingly used in applications such as adaptive radiotherapy and radiotherapy retreatment, and whilst they permit more accurate alignment of anatomical changes over time, the process contains some uncertainties and should be used carefully.