Colorectal cancer affects 29,000 people and kills approximately 15,000 in England and Wales each year, most of these deaths resulting from the effects of local or distant recurrence. There is a need to give these patients accurate prognoses and individualised treatment regimens. At present, the best prognostic markers are clinicopathological. Post-genomic science and the new high throughput technologies offer unrivalled opportunities to understand the biology and molecular pathology of colorectal cancer. These technologies should be used in the context of large randomised controlled trials to identify new molecular prognostic and predictive markers and also new targets for therapy.