Background Coronary artery disease (CAD) is one of the most prevalent cardiovascular diseases where serum lipoprotein oxidation plays a significant role. Polyunsaturated fatty acids (PUFA) n−6 : n−3 unbalance ratio consumption, affects lipoprotein oxidation, and inflammation processes. This study aimed to analyze the relationship between n−6 : n−3 PUFA ratio intake with oxidized lipoproteins in individuals with CAD. Methods A cross-sectional study was performed including 105 subjects (51 diagnosed with CAD and 54 non-CAD) from western Mexico. Dietary information was collected using a habitual day food record. Serum oxidized low-density lipoprotein (oxLDL) and oxidized high-density lipoprotein (oxHDL) concentrations were quantified by enzyme linked immunosorbent assay. Results CAD subjects had higher oxHDL/HDL cholesterol (HDL-c) ratio [0.102 (0.092–0.112) vs. 0.080 (0.070–0.090), P = 0.004] and oxLDL/LDL cholesterol (LDL-c) ratio [129.2 (108–150.4) vs. 59.7 (39.3–80), P < 0.001] compared to non-CAD subjects. Risk factors associated with CAD were a high n−6 : n−3 PUFA ratio (odds ratio, OR = 2.3, P = 0.046), hypoalphalipoproteinemia in men (OR = 3.2, P = 0.014), moderate/high tobacco index (OR = 6.33, P = 0.003), elevated waist circumference in women (OR = 7, P = 0.004), hypertension (OR = 21.14, P < 0.001), and type 2 diabetes (OR: 25, P < 0.001). The oxHDL/HDL-c ratio was positively associated with the n−6 : n−3 PUFA ratio [r 2 = 28.3, B = 0.002 (0.001–0.003), P < 0.001] in CAD patients. Conclusions This study showed that a higher n−6 : n−3 PUFA ratio intake correlates with higher serum oxHDL/HDL-c in CAD patients.
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