Lipoprotein(a) [Lp(a)], a low-density lipoprotein-like particle, is recognized as an independent risk factor for atherosclerosis, cardiovascular diseases, and diabetic vascular diseases. Our recent studies revealed that the single nucleotide polymorphisms (SNPs) of peroxisome proliferator-activated receptors (PPAR alpha/delta/gamma) gene are involved in the regulation of lipid storage and metabolism. In order to investigate the relationships between the SNPs of PPAR alpha/gamma gene and plasma levels of Lp(a), 644 participants were randomly selected from Chinese Han population in the present study. As the results shown, Lp(a) was significantly associated with L162V (rs1800206) in PPAR alpha. Compared with those subjects with widetype (LL), significantly higher Lp(a) concentration was determined in the individuals with mutant (LV + VV) (mean difference: 49.07 mg/l, 95 % CI 23.32-74.82 mg/l, p = 0.0002). Moreover, with generalized multifactor dimensionality reduction analysis, our present results indicated that there was a significant association between plasma Lp(a) level and gene-gene interaction among the polymorphisms rs1800206, rs135539 in PPAR alpha and rs10865710, rs1805192, and rs4684847 in PPAR gamma. Therefore, our presented study indicated that PPAR alpha/gamma polymorphisms should be involved in the regulation of plasma Lp(a) in independently and/or in an interactive manner, suggesting that PPAR alpha/gamma gene may influence the risk of hypertension, cardiovascular diseases, and dyslipidemia by regulating Lp(a) level.