Different clinical studies have demonstrated that fish oil, rich in the very-long-chain ω-3 polyunsaturated fatty acids (PUFAs), has immunomodulatory effects, suppressing the production of pro-inflammatory cytokines in diverse groups of critically ill patients. Moreover, such compounds have been found to attenuate the inflammatory response within 2-3 days upon parenteral administration. Recent experimental data suggest that activation of the cholinergic anti-inflammatory pathway constitutes a novel mechanism of such immune-regulatory effects. Since enhanced vagal tone has been associated with decreased cytokine secretion, novel monitoring tools of its activity at the bedside are needed, in order to evaluate nutritional manipulation of inflammatory response in the critically ill. The present chapter provides an overview of the mechanisms of action through which ω-3 PUFA modulates immune response in critically ill patients suffering from sepsis and septic shock. Furthermore, it summarizes the current evidence regarding clinical effects from administration of fish oil rich in ω-3 PUFAs in septic patients. Finally, it presents data that suggest the existence of a continuous interrelation between immune status and autonomic nervous system during systemic inflammation and proposes novel tools of autonomic nervous system monitoring at the bedside, in order to assess pharmacological manipulation of immune response by ω-3 PUFAs in acute illness.