Hyperhomocysteinemia is recognized as an independent risk factor for cardiovascular disease, especially atherosclerosis, in adult patients with chronic renal failure (CRF). However, there is little information about the relationship between plasma homocysteine levels and left ventricular hypertrophy. The aim of this study was to determine plasma homocysteine levels and risk factors for left ventricular hypertrophy and to investigate the relationship between plasma homocysteine concentration and left ventricular mass index (LVMI) in children with CRF. The homocysteine level was measured by high-performance liquid chromatography and LVMI was calculated using echocardiographic findings in 27 children with CRF and 16 healthy controls. The mean LVMI and mean plasma homocysteine concentration in the CRF group, especially in patients with end-stage renal disease, were statistically higher than the control group (P<0.05). There was no correlation between LVMI and plasma homocysteine concentration. There was a positive correlation between plasma homocysteine concentration and serum creatinine level. There was a positive correlation of LVMI with creatinine and blood pressures (systolic, diastolic, and mean arterial pressure). There was a negative correlation of LVMI with hemoglobin level in multiple linear regression analysis. In our view homocysteine does not have a direct effect on left ventricular structure and left ventricular hypertrophy is the end organ damage associated with hypertension, anemia, and CRF. More prospective studies are needed to better clarify the inter-relationships of plasma homocysteine level and left ventricular structure in children with CRF.