Background: Dipeptidyl peptidase-4 (DPP4) can influence lipid homeostasis and atherosclerosis progression. Our aim was to assess the association of DPP4 gene polymorphisms with hypoalphalipoproteinemia and DPP4 levels, in a cohort of Mexican individuals.Methods: Five DPP4 polymorphisms (rs12617336, rs12617656, rs1558957, rs3788979, rs17574) were genotyped in 748 participants with and 745 without hypoalphalipoproteinemia. The associations were evaluated using logistic regression analyses.Results: Under inheritance models adjusted for confounding variables, the rs12617336 (OR = 0.22, Pheterozygote = 0.001) and rs17574 (OR = 0.79, Padditive = 0.033; OR = 0.75, Pdominant = 0.021; OR = 0.75, Pheterozygote = 0.029; OR = 0.74, Pcodominant1 = 0.024) polymorphisms were associated with a low risk of hypoalphalipoproteinemia. Moreover, GTTCG haplotype was also related with a low risk of this condition (OR = 0.75, P = 0.021). Additionally, both polymorphisms were associated with protection for the presence of insulin resistance (IR) (OR = 0.17, Pheterozygote = 0.019 for rs12617336 and OR = 0.75, Padditive = 0.049 for rs17574). The rs12617336 was also associated with a low risk of hyperinsulinemia (OR = 0.11, Pheterozygote = 0.006). Difference in DPP4 levels were observed in individuals with rs17574 genotypes, the rs17574GG genotype individuals had the lowest levels.Conclusions: Our data suggest that rs12617336 and rs17574 DPP4 polymorphism could be envisaged as protective genetic markers for hypoalphalipoproteinemia, IR, and hyperinsulinemia. The rs17574GG genotype was associated with the lowest DPP4 levels.