Dietary n-3 polyunsaturated fatty acid (PUFA) exerts anti-inflammatory and immunoregulatory effects via downregulation of the innate and adaptive immune responses. However, the effect of dietary n-3 PUFA on experimental Crohn's Disease (CD) in rats and the underlying mechanisms are unclear. The present study aimed to investigate the effects of n-3 PUFA on CD induced by 2,4,6-trinitrobenzene sulfonic acid (TNBS) in rats, and to determine the underlying mechanisms, including the peroxisome proliferator-activated receptor (PPAR)-gamma and nuclear factor of activated T-cells (NFAT) pathway. Sprague-Dawley rats (n=90) were randomly assigned to the following groups: Control (intragastric distilled water); PUFA control (intragastric n-3 PUFA, 20 mg/kg/day); trans-fatty acid (TFA) control (intragastric TFA, 13 mg/kg/day); model (intragastric distilled water + TNBS); PUFA model (intragastric n-3 PUFA, 20 mg/kg/day + TNBS); and TFA model (intragastric TFA, 13 mg/kg/day + TNBS). The disease activity index (DAI), colon macroscopic damage index (CMDI) and tissue damage index (TDI) were evaluated. The expression of PPAR-gamma, NFAT, interleukin (IL)-4 and IL-2 mRNA in colonic tissues was determined by reverse transcriptionquan-titative polymerase chain reaction (RT-qPCR), and the serum levels of IL-6, IL-12, tumor necrosis factor-a and interferon-gamma were measured by ELISA. The results demonstrated that dietary n-3 PUFA markedly attenuated colonic inflammation compared with the model group, as indicated by reduced DAI, CMDI and TDI scores, amelioration in pathological evaluation and improvements in localized mucosal inflammation, as indicated by the levels of cytokines associated with local mucosal immunity. Treatment with n-3 PUFA increased the gene expression of PPAR-gamma in TNBS-treated rats, and reduced the expression of NFAT, which ultimately reduced the release of IL-4 and IL-2 detected by RT-qPCR. A TFA-enriched diet was observed to increase DAI and TDI scores, aggravate pathological inflammation with epithelioid granulomas and enhance the release of proinflammatory cytokines, compared with the model group. In conclusion, the present study demonstrated that dietary n-3 PUFA may attenuate experimental CD induced by TNBS in rats by regulating the expression and activity of the PPAR-gamma/NFAT signaling pathway. These results provide a promising potential therapeutic method for the treatment of CD.