Objective To explore the effect omega-3polyunsaturated fatty acid omega-3 FA on clinical manifestations of gastrointestinal toxicity and quality of life (QOL) induced by chemotherapy for patients with gastric or colorectal cancer. Methods After screening chemotherapy, Fifty patients with gastric or colorectal cancer, according to developing WHO side-effect grading system of grade 2 or higher were randomly divided into either control group (n=25) or omega-3 FAs group (n=25) during next cycle of chemotherapy. In the control group, the patients received the same chemotherapy regimens as screening cycle and in the omega-3 FA group, received chemotherapy and omega-3 FAs. Prophylactic intravenous 200 mL /d was given for 5 days. The gastrointestinal complications such as nausea,vomiting or diarrhoea and Karnofsky performance status(KPS ),IL-2,IFN-γandCRP,ect, were evaluated respectively. Results Compared with the control group, the scores of nausea vomiting and diarrhea and IL-2,IFN-γor CRP levels decreased , significantly,on the contrary, the score of QOL increased. There was significantly statistical difference (P<0.05). Conclusion Prophylactic intravenous omega-3 FA can ameliorate clinical manifestations of gastrointestinal toxicity and systemic inflammatory response syndrome(SIRS) induced by chemotherapy and improve QOL for patients with gastric or colorectal cancer.