Sepsis is a systemic inflammatory reaction, which is aggravated by aspects of the immune response that are thought to be inhibited by Omega-3 fatty acids. The aim of the present study was to determine if Omega-3 fatty acid could modulate immunological function and improve survival rate among septic patients with intestinal dysfunction. A total of 48 mechanically ventilated patients with intestinal dysfunction were included in this prospective, randomized and single-blind clinical study. Patients were randomly divided into control (group A) and treatment groups (group B). The treatment protocol for all the participants followed the Sepsis Survival Campaign guidelines, and group B received total parenteral nutrition containing 100 ml of Omega-3 fatty acids (containing 10 g refined fish oil) per day in addition to the standard treatment applied in group A. Group B had a significantly lower mortality rate compared with group A (12.5 vs. 41.7%, P<0.05) during the 28-day follow-up. Group B also had lower Acute Physiology and Chronic Health Evaluation II scores (P<0.05) and lower Marshall scores (P<0.05) at day 7. In addition, group B had a higher ratio of T helper to inducer lymphocytes as well as a higher ratio of CD4 to CD8 lymphocytes (P<0.01 for both) than group A. It was concluded that Omega-3 fatty acids improved T helper/inducer and CD4/CD8 ratios, and may have reduced mortality, among septic patients with intestinal dysfunction.