Image registration techniques spatially register clinical images of patients performed either at different times with the same modality (intra-modality) or with different modality (inter-modality), to facilitate assessment of change and to take full advantage of the frequently complementary information provided by the imaging modalities. Inter-subject registration permits comparison to normal data bases and averaging of data from several subjects to improve statistical significance. Image registration is well established in the brain since the skull limits deformation of the brain between studies and the use of rigid body transformation can usually be justified for intra-subject registrations. A large range of image registration algorithms, ranging from completely manual to fully automatic, have been developed. These can be classified into external methods, which typically use fiducial markers, intrinsic techniques, which rely on the information contained in the patient image data and non- image based methods, which use information external to the data being registered. The technique of choice depends on the specific requirements of the application and it is unlikely that a single `best' technique can meet sometimes conflicting requirements (e.g. accuracy, speed, ease of use etc). While considerable progress has been made in image registration outside the brain, considerable challenges still remain. In this paper, we present the basic principles of image registration and practical issues arising from our experience with routine clinical use of image registration over several years.