Background: Paraoxonase-1 (PON1) moves with high-density lipoprotein (HDL) particles in blood and prevents low-density lipoprotein (LDL) particles from oxidation. The aims of this study were to investigate the correlation between fatty acid composition of HDL phospholipids with pon-1 polymorphisms and response to lovastatin treatment in people with high blood cholesterol. Methods: In this descriptive study, 265 patients were selected and divided into two groups based on LDL-C concentrations; 131 patients with LDL-C greater than 130 mg/dl (cases) and 134 patients with LDL-C lower than 130 mg/dl (controls). Fatty acids of HDL phospholipids were measured with gas chromatography and lipid profile (cholesterol, triglyceride, LDL-C, HDL-C), apolipoprotein A1 and apolipoprotein B were measured by relevant commercial kits. Oxidized LDL was measured by ELISA method and activity of paraoxonase was determined by a relevant standard manual method. Genotypes of L55M polymorphism were determined by polymerase chain reaction-restriction fragment length polymorphism procedure. Results: Prevalence of L allele from L55M polymorphism was 0.65 and 0.53 in the case and control groups, respectively (P=0.04). PON1 paraoxonase activity in LL homozygote genotype was higher than other genotypes upon treatment with lovastatin. Concentrations of oleic, linoleic and eicosapentaenoic acids in LL genotype were increased by lovastatin administration. Conclusion: Allele (L) from L55M polymorphism had a higher frequency in patients with higher LDL-C concentrations. PON1 genotypes seemed to have a modifying role on paraoxonase-1 activity after lovastatin therapy.