Abstract: Metabonomics is a novel subject which develops after genomics, transcriptomics and proteomics. With its unique advantage, metabonomics has been used widely in screening diagnostic biomarker in a variety of tumors. At present, some diagnostic biomarkers are found in tissue, serum samples, urine samples and stool specimens of gastrointestinal cancer patients by metabonomics, which maybe helpful for the early diagnosis and individualized treatment of gastrointestinal cancer.