Background Many genetic polymorphisms and clinical laboratory parameters have been shown to be associated with ischemic stroke (IS). However, these results are often inconsistent. Therefore, the aim of the study was to evaluate the correlation between clinical laboratory parameters, the risk genetic polymorphisms and IS in Shanghai population.Methods The clinical laboratory parameters were measured by automatic biochemical analyzer. The genotype frequencies and allelic frequencies of the polymorphisms gene encoding angiotensin-converting enzyme ( ACE D/I), gene encoding methylene tetrahydrofolate reductase ( MTHFR C677T), gene encoding β-fibrinogen 455/148 ( β-Fg -455/148) were characterized by restricted fragment length polymorphisms-polymerase chain reaction (RFLP-PCR). The gene encoding plasminogen activator inhibitor ( PAI -1 4G/5G) and gene encoding apolipoprotein E 2,3,4 ( ApoE ε2,3,4) were characterized by allele specific PCR. The genotype frequency and allele frequency of the 6 risk genes of IS were analyzed by chi-square test in different groups of laboratory indexes. The distribution maps of the polymorphisms ACE D/I, MTHFR C677T, β-Fg -455 A/G, β-Fg -148 T/C, PAI -1 4G/5G, ApoE ε2,3,4 and clinical laboratory paramaters were compared between healthy people and patients with IS.Results The laboratory parameters were related to ACE I/D, β-Fg -455 A/G, and PAI -1 4G/5G genes. D allele of ACE I/D was associated with high levels of total cholesterol (TC) and Low-density lipoprotein (LDL). High levels of fasting blood glucose (FBG), triglyceride (TG), and LDL were risk factors for IS. There were significant differences in genotype frequencies of ACE I/D, β-Fg -455 A/G, and β-Fg- 148 T/C genes between IS and control group.Conclusions Clinical laboratory paramaters are associated with the risk genes polymorphisms of IS. It is suggested that control value of clinical laboratory paramaters should be determined according to the genotype carried by the patients with diabetes and hyperlipidemia when preventing IS.