The purpose of this study was to investigate the expression of S100A12 on the surface of circulating endothelial cells (CECs) in children with Kawasaki disease (KD) and the correlations between S100A12 and coronary artery lesions (CALs). The ratio of CECs to mononuclear cells (CECs/MNC), the positive rate of S100A12 on CECs surface (CECs-S100A12/CECs), and the fluorescence intensity of S100A12 on CECs surface (FI-S100A12-CECs) were evaluated respectively in 42 patients with acute stage (A-KD), subacute stage (SA-KD) and convalescent stage KD (C-KD). The CECs/MNC ratio increased significantly in patients with A-KD and SA-KD with CALs. The CECs-S100A12/CECs rate and FI-S100A12-CECs level were significantly higher in patients with KD than in the controls. The FI-S100A12-CECs level decreased to near half levels in patients with SA-KD and C-KD without CALs, but increased continuously in patients with SA-KD with CALs. The CECs/MNC ratio and FI-S100A12-CECs level in patients with SA-KD with CALs were significantly higher than in patients with SA-KD without CALs. The FI-S100A12-CECs level was significantly higher in patients with C-KD with CALs than in C-KD without CALs. The S100A12 expression on the CECs surface increased significantly in patients with KD and persisted for a longer time in patients with CALs, suggesting that the S100A12 expression on CECs may be involved in the development of CALs.