Tight junction proteins are important for intestinal homeostasis. They prevent paracellular transport of large molecules and maintain cell polarity. Impaired tight junction function leads to a more permeable intestinal epithelial barrier and therefore potentially increases disease risk. Limited information is available concerning the effects of food components on the intestinal barrier, particularly paracellular permeability and tight junction proteins. In vitro studies with intestinal epithelial cells and in vivo studies using animal models have demonstrated that dietary n-3 and n-6 polyunsaturated fatty acids (PUFAs), particularly n-3, can reduce intestinal inflammation and permeability. PUFAs can induce transcriptional regulators which may act in combination with their target molecules in defense against oxidative stress, thereby maintaining the intestinal barrier function. More studies that take into account the type and/or amount of individual fatty acids are needed in order to elucidate the molecular mechanisms of PUFAs on intestinal epithelial barrier function.