Gastrointestinal (GI) carcinoma is a common malignant disease worldwide. Its development and progression is a multistage process involving a multifactorial etiology. Although the detailed mechanisms of the development of GI carcinoma remain controversial, the elucidation of its molecular biology over the last few years has resulted in a better perspective on its epidemiology, carcinogenesis and pathogenesis. More significantly, it is currently possible to use biological indicators or biomarkers in differential diagnosis, prognostic evaluation and specific clinical interventions. In this review, we aimed to describe the biomarkers of pathogenesis, invasion, metastasis and prognosis of GI carcinoma and discuss their potential clinical applications. The majority of these biomarkers, such as tumor-associated antigens, oncogenes and tumor suppressor genes, metastasis-associated genes, cell adhesion molecules, cytokines, growth factors and microRNAs, are currently broadly applicable.