This study was conducted to determine the effects of omega-3 fatty acids and vitamin E co-supplementation on gene expression of lipoprotein(a) (Lp[a]) and oxidized low-density lipoprotein (Ox-LDL), lipid profiles and biomarkers of oxidative stress in women with polycystic ovary syndrome (PCOS). This randomized double-blind, placebo-controlled trial was done on 68 women diagnosed with PCOS according to the Rotterdam criteria aged 18-40 years old. Participants were randomly assigned into two groups to receive either 1000 mg omega-3 fatty acids from flaxseed oil containing 400 mg α-Linolenic acid plus 400 IU vitamin E supplements (n = 34) or placebo (n = 34) for 12 weeks. Lp(a) and Ox-LDL mRNA levels were quantified in peripheral blood mononuclear cells of PCOS women with RT-PCR method. Lipid profiles and biomarkers of oxidative stress were quantified at the beginning of the study and after 12-week intervention. Quantitative results of RT-PCR demonstrated that compared with the placebo, omega-3 fatty acids and vitamin E co-supplementation downregulated expressed levels of Lp(a) mRNA (P < 0.001) and Ox-LDL mRNA (P < 0.001) in peripheral blood mononuclear cells of women with PCOS. In addition, compared to the placebo group, omega-3 fatty acids and vitamin E co-supplementation resulted in a significant decrease in serum triglycerides (-22.1 ± 22.3 vs. +7.7 ± 23.6 mg/dL, P < 0.001), VLDL- (-4.4 ± 4.5 vs. +1.5 ± 4.7 mg/dL, P < 0.001), total- (-20.3 ± 16.6 vs. +12.2 ± 26.1 mg/dL, P < 0.001), LDL- (-16.7 ± 15.3 vs. +11.9 ± 26.1 mg/dL, P < 0.001) and total-/HDL-cholesterol (-0.5 ± 0.6 vs. +0.4 ± 0.8, P < 0.001). There were a significant increase in plasma total antioxidant capacity (+89.4 ± 108.9 vs. +5.9 ± 116.2 mmol/L, P = 0.003) and a significant decrease in malondialdehyde levels (-0.3 ± 0.4 vs. -0.008 ± 0.6 μmol/L, P = 0.01) by combined omega-3 fatty acids and vitamin E intake compared with the placebo group. Overall, omega-3 fatty acids and vitamin E co-supplementation for 12 weeks in PCOS women significantly improved gene expression of Lp(a) and Ox-LDL, lipid profiles and biomarkers of oxidative stress.