The objective of current study was to assess the gender differences on the lipid profiles, apoprotein B, and body composition among the subjects with metabolic syndrome after daily walnut intake (45 g) for 16 weeks. 89 participants (44 men, 40±6.2yr) with metabolic syndrome were screened if they meet at least three metabolic syndrome components out of five diagnosis criteria (i.e., waist circumstance ≥90cm for men and ≥85cm for women, blood pressure 130/85mmHg or higher, HDL-cholesterol ≤40mg/dL for men and ≤50mg/dL for women, triglyceride level ≥150mg/dL, and fasting blood glucose ≥100mg/dL). Blood lipid profiles (consisting of triglyceride, total cholesterol, HDL-cholesterol, and LDL-cholesterol), apoprotein B, fasting blood sugar, anthropometric measurement, bioimpedance analysis, and blood pressure were measured at baseline and week 16. The significance of the differences between baseline and week 16 were analyzed using the paired t-test or Wilcoxon signed-rank test, as appropriate (p<0.05). Body protein of male and all subjects at week 16 was significantly higher compared to the baseline (p=0.026, p=0.039, respectively), whereas no significance among female subjects (p=0.876). Male showed significantly increased basal metabolic rate at week 16 (p=0.017), but not significant among female subjects (p=0.581) and all subjects (p=0.12). Waist circumstance among female and all subjects were significantly lower compared to baseline (p=0.036 and 0.026, respectively), and marginally significant among male subjects (p=0.050). LDL-cholesterol and total cholesterol levels were significantly decreased among male subjects (p=0.011 and 0.003, respectively), whereas those among female subjects were not significantly different (p=0.307, and 0.072, respectively). Triglyceride level was significantly decreased among female subjects compared with baseline (p=0.007) by Wilcoxon test. The positive change of apoprotein B among male and all subjects were significant compared with the baseline (p=0.001 and 0.003, respectively), whereas those among female subjects were not significant (p=0.282). The results suggest that daily walnut consumption for 16 weeks may increase body protein and basal metabolic rate, and decrease the levels of LDL-cholesterol, cholesterol and apoprotein B among male subjects with metabolic syndrome. Also, daily walnut intake may decrease waist circumstance and triglyceride level among female subjects with metabolic syndrome.