BACKGROUND: Oxidative stress has recently been shown to play an important role in the development of arteriosclerosis in patients with Kawasaki disease (KD); however, no study has investigated this association in early childhood patients with KD. In this study, we evaluated prospectively the association between the levels of oxidative stress and the endothelial function in early childhood patients with KD. METHODS: We compared the derivatives of reactive oxygen metabolites (ROM), flow-mediated dilatation (FMD), and biological characteristics in a population of 50 children: 10 patients with KD and coronary artery lesions (CAL) (group 1), 15 KD patients without CAL (group 2), and 25 healthy age- and sex-matched children (group 3). RESULTS: The median age of all KD children at study enrollment was 6.8 (IQR 4.4-8.2) years. ROM levels were significantly higher in group 1 (p <  0.001) and group 2 (p = 0.004) than in group 3. The %FMD of group 1 (p <  0.001) and group 2 (p = 0.026) was significantly lower than that of group 3. There was a significant negative correlation between ROM and %FMD (r = - 0.60, p <  0.001). A multiple linear regression analysis identified ln-ROM (standardized coefficient = - 0.403, p = 0.043) and total fever duration (standardized coefficient = - 0.413, p = 0.038) as significant determinants of %FMD in the patients with KD. CONCLUSIONS: Our study suggests that oxidative stress is strongly associated with endothelial dysfunction in early childhood patients with KD. Furthermore, we found that the longer the fever duration, the higher the risk of oxidative stress-induced endothelial dysfunction in these children.