We sought to determine flow-mediated vasodilatation (FMD) of the brachial artery and to assess the relationship of FMD with multiple demographic, clinical and biochemical parameters and cardiac and vascular structure and function in children with chronic kidney disease (CKD) stages 2-4. Forty-three patients, aged 6-20 years, with CKD [mean glomerular filtration rate (GFR) 47 +/- 21 ml/min per 1.73 m2 body surface area, range 16-89 ml/min per 1.73 m2] and 34 healthy age-matched controls were included and studied cross-sectionally between 2001 and 2005. The peak FMD was similar in the CKD and control subjects (mean 6.3% vs 6.7%, P = 0.85). However, abnormally low FMD (< 1.1%) was found in ten (23%) children with CKD. Among children with CKD, those with low FMD were younger, shorter, lighter, and had lower body mass index (BMI) than children with normal FMD, but the difference reached statistical significance only for weight and BMI. Serum triglyceride levels were significantly lower in those with low FMD; otherwise, the two groups were similar with respect to multiple clinical and biochemical parameters. Cardiac and vascular structure was similar in children with normal and low FMD. In conclusion, children with CKD stage 2-4 appear to have increased prevalence of decreased FMD of the brachial artery. However, our study identified few significant factors associated with low FMD in children with CKD.