Defects in tight junction barrier have been considered as an important etiologic factor of Crohn's disease. n-3 polyunsaturated fatty acids (PUFAs) exert beneficial effects on inflammatory bowel disorders. However, the mechanisms remain unknown. We found that docosahexaenoic acid (DHA, 22:6 n-3) and eicosapentaenoic acid (EPA, 20:5 n-3) changed lipid environment in membrane microdomains of tight junction in vitro. n-3 PUFAs treatment effectively prevented the redistribution of occludin and ZO-1 and distortion of TJ morphology, reduced transepithelial electrical resistance induced by IFN-γ and TNF-α. We also observed dramatic reorganization of TJ proteins in epithelial lateral membrane following treatment with these cytokines. Our findings for first time indicate that n-3 PUFAs play an important role in proinflammatory cytokines-induced permeability defects and epithelial barrier dysfunction by modifying lipid environment in membrane microdomains of tight junction.