We investigated the relationship between endothelial constitutive nitric oxide synthase (ecNOS) gene polymorphism and lipid metabolism in patients with nondiabetic chronic renal failure on hemodialysis. Serum from 181 nondiabetic patients on hemodialysis were examined. A genomic DNA fragment was amplified by polymerase chain reaction (PCR) for determining the ecNOS genotype. The PCR products were designated as a and b alleles by electrophoresis. In hemodialysis patients, the frequency of the ecNOS4 for b/b, b/a and a/a genotype was 76.6, 22.8 and 0.6%, respectively. There was not significant difference in the levels of total cholesterol (TC), triglyceride (TG) and calculated low-density lipoprotein cholesterol (LDL-c) in sera between patients (aa and ba) with the a allele and patients (bb) without the a allele. On the other hand, the levels of serum high-density lipoprotein cholesterol (HDL-c) in patients with the a allele (51.9 ± 3.33 mg/dl) were significantly higher than those in patients without the a allele (43.05 ± 1.40 mg/dl) (p = 0.005). The frequency of patients with the a allele and low levels of serum HDL-c among patients with a long duration of dialysis (≧10 years) was significantly lower than that in patients with short duration of dialysis (<10 years) (p = 0.05). It appears that an intron 4 gene polymorphism in ecNOS may modulate lipid metabolism in nondiabetic patients on hemodialysis and the a allele of ecNOS gene polymorphism may affect the prognosis of hemodialysis patients with low levels of serum HDL-c.