Every year approximately 2 million Europeans develop a malignancy; the group of gastrointestinal cancers is the single largest group, with approximately 600,000 new cancers annually. Despite recent innovations and developments in the diagnosis and management of these cancers, prognosis remains poor and treatment options limited. In recent years, new technological advances in proteome analysis and its application to patient management have been made and are the subject of ongoing clinical studies. The identification of biomarkers and biomarker patterns has raised hope that noninvasive diagnosis of cancers in their early stages may soon be an option. However, before the results of proteome analysis can be implemented in the management of cancer patients, further validation of these markers and the issues of sensitivity, specificity, reproducibility and accuracy need to be addressed and solved.