Background: The aim of this study was to test whether or not infusion of triglycerides containing ω-3 fatty acids (FAs) modifies immune function in terms of systemic clearance and organ distribution of injected Escherichia coli in a rabbit model. Materials and Methods: In groups of 6 rabbits each, a defined number of E. coli (1.3 × 108 colony-forming units, CFU) was injected intravenously after 3 days of infusion with a lipid emulsion prepared from fish oil (Omegavenös® 10%, 1.5 g/kg body weight/day), a soy oil preparation (Lipovenös® 10%, 1.5 g/kg body weight/day), or after isotonic saline application (control). In order to compare dose-dependent effects, in a second experimental design a lower dose of each lipid emulsion (0.5 g/kg body weight) was infused over a 4-hour period before applicating E. coli . Parameters monitored were arterial pressure and rates of bacterial elimination from the blood. The animals were killed 3 h and 6 h after bacterial infection, respectively, and tissue samples of liver, spleen, lung, and kidney were collected for microbiological examinations. Results: Lipovenös infusion produced a significant delay in blood clearance compared with saline and Omegavenös treatment. The diminished systemic bacterial elimination after Lipovenös infusion was accompanied by increased numbers af viable bacteria in lung and spleen. In contrast to this, in the Omegavenös group bacterial counts in the lung did not increase and smaller amounts of viable bacteria were detected in organ homogenates 6 h after injection of E. coli . Conclusion: Compared with the soy oil preparation, ω-3 FAs induce improved bacterial clearance from the blood that is associated with significantly lower numbers of E. coli in the lung. Thus, appropriate nutrition providing ω-3 FA might serve as a pharmacological tool to improve host defence against bacterial infection in critically ill patients.