Background Kawasaki disease (KD) is an acute, self-limited, systemic vasculitis of unknown etiology. In the present study, we investigated whether there is a relationship between KD and dynamic thiol/disulphide homeostasis. Methods This case-control study involved KD patients and healthy controls. Plasma total, native and disulphide thiol and the disulphide/native, disulphide/total and native thiol/total thiol ratios of all patients and the control group were analyzed simultaneously. Results A total of 20 patients with KD (male/female, 12/8) and 25 age- and gender-matched healthy controls (male/female, 12/13) were evaluated. Native, total thiol and native thiol/total thiol ratio were significantly lower in KD patients than in the control group (P < 0.001). In contrast, disulphide thiol, disulphide/native thiol and disulphide/total thiol ratios were significantly higher in KD patients than control subjects (P < 0.001). In KD patients with coronary artery lesion (CAL), the native thiol and total thiol were significantly lower than in KD patients without CAL. In KD patients with CAL, the ratios of disulphide/total thiol and disulphide/native thiol were significantly higher than in those without CAL (P = 0.02 and P = 0.02, respectively), whereas the ratio of native/total thiol was significantly lower (P = 0.02). Conclusion The KD patients had lower plasma thiol (native and total) and higher disulphide thiol than controls, indicating that dynamic thiol/disulphide homeostasis might be an important indicator of inflammation in KD. Alteration and shifting of thiol/disulphide homeostasis to the oxidized side are correlated with the pathogenesis of KD and CAL.