Dyslipidemia is an important risk factor for myocardial infarction (MI). We previously showed that gene polymorphisms associated with MI differed among individuals with different lipid profiles. We also showed that rs6929846 of BTN2A1 and rs2569512 of ILF3 were significantly associated with MI in Japanese individuals. In the present study, we examined the relationship between rs6929846 of BTN2A1 or rs2569512 of ILF3 and MI in individuals with low or high serum concentrations of triglycerides, high density lipoprotein (HDL) cholesterol, or low density lipoprotein (LDL) cholesterol, respectively. The study population comprised 5513 unrelated Japanese individuals, including 1537 subjects with MI and 3976 controls. Multivariable logistic regression analyses with adjustment for covariates revealed that rs6929846 of BTN2A1 was significantly associated with MI in individuals with low (P=3.1 x 10-5; odds ratio, OR=1.66) or high (P = 1.1 x 10⁻⁶; OR = 2.09) triglycerides; in individuals with low (P = 0.0082; OR = 1.75) or high (P = 2.0 x 10⁻⁹; OR = 1.85) HDL cholesterol; and in individuals with low (P = 3.2 x 10⁻⁷; OR = 1.75) or high (P = 2.8 x 10⁻⁵; OR =2.18) LDL cholesterol. Similar analyses revealed that rs2569512 of ILF3 was significantly associated with MI in individuals with low (P = 0.0066; OR = 1.47) or high (P = 0.0013; OR = 1.88) triglycerides; in individuals with low (P = 0.0059; OR = 1.96) or high (P = 0.0020; OR = 1.51) HDL cholesterol; and in individuals with low (P = 0.0004, OR = 1.62) LDL cholesterol, but not in those with high LDL cholesterol. The results suggest that the relationship between rs6929846 of BTN2A1 or rs2569512 of ILF3 and MI is influenced by the serum concentrations of HDL and LDL cholesterol, respectively. Stratification of subjects according to lipid profiles may thus be useful for the personalized prevention of MI based on genetic information.