Background: Nutritional support plays an essential role for recovery in infants who undergo gastrointestinal surgery. The current standard type of intravenous lipid emulsion (IVLE) used as parenteral nutrition is the mixture of medium-chain triglyceride (MCT) and long chain triglyceride (LCT) rich in ω-6. Studies showed that ω-6 is associated with higher level of proinflammatory cytokines, leading to increased mortality rate, morbidity rate, and postoperative recovery time. The latest generation of emulsion is a mixture of MCT, LCT, olive oil (OO), and fish oil (FO) which may optimize the ω6/ω3 ratio. This study aimed to compare the effect of MCT/LCT/OO/FO IVLE to standard IVLE on IL-1β, IL-8 and plasma fatty acids in infants who had undergone gastrointestinal surgery. Methods: A single-blind, randomised controlled, pretest-posttest design study was done in twelve subjects that were classified into two groups. Group 1 received standard IVLE, group 2 received MCT/LCT/OO/FO IVLE. The type of standard and MCT/LCT/OO/FO IVLE used in this study were Lipofundin 20% and SMOFlipid 20%, respectively, both administered for three consecutive days in 1-4 gram/kilogram/day. IL-1β and IL-8 were examined using ELISA while fatty acids was analyzed using gas chromatography tandem mass spectrometry (GC-MS). Statistical analyses were performed using SPSS for Mac 23. Results: No statistical difference was found in age, gender, birth weight and diagnosis between both groups. Leukocyte was significantly lower in MCT/LCT/OO/FO group 3 days after surgery (p=0.025). CRP was lower in MCT/LCT/OO/FO group 3 days after surgery (p=0.01) and in changes within 3 days (p=0.016). There were no differences in IL-1β, IL-8 and ω-3 but ω-6 was higher in standard IVFE group on third day after surgery (p=0,048) Conclusion: MCT/LCT/OO/FO IVLE can significantly lower leukocyte, CRP and ω-6 levels and is comparable with standard IVLE on IL-1β, IL-8 and ω-3 levels in infants underwent gastrointestinal surgery.