Genetic aberrations in cancer cells can be of immediate relevance to the patient. They enable definitive diagnoses to be reached and sub-classification of certain tumour types into good or bad prognostic groups, information which can influence therapy. These aberrations can also be used as tumour markers for monitoring the response to therapy. Major technological advances in the last few years have facilitated these applications in the routine clinical setting and encouraged searches for new genetic markers. As the genes directly affected are identified and their roles in tumorigenesis elucidated, they are likely to provide novel targets for therapeutic intervention.