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Perilla (<i>Perilla frutescens</i>) oil reduces high-fat-diet-induced colon inflammation by suppressing the NF-κB pathway. In the current study, we compared the effect of endogenously produced and externally supplemented omega-3 fatty acids on high-fat-diet-induced colon inflammation. The <i>fat-1</i> transgenic mice that endogenously synthesize omega-3 fatty acids were backcrossed with C57BL/6J wild-type mice to obtain transgenic (TR) and wild-type (WT) littermates. Five-week-old male littermates were divided into five groups: two groups fed 10% normal diet (WTLD, TRLD) and three groups fed with a 60% fat high-fat diet (WTHD, TRHD, and WTPO). In the WTPO group, 8% (<i>w</i>/<i>w</i>) of perilla oil was added. Perilla oil supplemented WT mice and <i>fat-1</i> transgenic mice suppressed high-fat-diet-induced body weight and improved serum lipid levels. Furthermore, the WTPO and TRHD groups exhibited increased colon length, lower macroscopic scores, and reduced levels of pro-inflammatory markers and improved epithelial integrity barrier markers. The expression of GPR120 was increased in the WTPO group. Altogether, our results indicated that perilla oil could improve the symptoms of colon inflammation as an alternate omega-3 fatty acid supplement.