Objective:To seek any relationship between the single nucleotide polymorphisms (SNPs) of the apolipoprotein E (ApoE) gene and blood lipid sensitivity to high-intensity interval training (HIIT).Methods:Two hundred and thirty Han Chinese college students (104 males and 126 females) who were not majoring in sports were recruited to perform a 28-minute high-intensity interval workout three times per week for 12 weeks. Before and after the intervention, blood levels of triglycerides (TG), high density lipoprotein cholesterol (HDL-C), low density lipoprotein cholesterol (LDL-C), and total cholesterol (TC) were measured. The subjects′ DNA was genotyped to obtain SNP loci, and a linear regression model was constructed to quantify any association between ApoE genotypes and phenotypes.Results:(1) A total of 21 SNP loci were identified associated with ApoE genes, one of which (rs7412) was found to be correlated with the training effect on blood lipids. (2) The initial TT and LDL-C values of carriers of the T allele of gene rs7412 (individuals with the CT + TT genotypes) were, on average, significantly lower than those of CC genotype individuals. However, no significant differences in the initial TG and HDL-C values among different genotypes were observed. (3) After the training the average LDL-C levels among the ApoE rs7412 polymorphic groups had changed significantly, with a significantly greater decrease observed among the carriers of the T allele compared with those of CC genotype.Conclusions:ApoE polymorphism may be significantly associated with TT and LDL-C values in Han Chinese youth, with carriers of the T allele tending to display lower levels than those of CC genotype. The polymorphism of ApoE gene rs7412 may be related to LDL-C reduction through HIIT, with carriers of the T allele more sensitive to such training.