this study was to investigate the correlation of vagal activity with coronary artery lesion (cAL) in Kawasaki disease (KD) children, and assess the predictive value of heart rate deceleration capacity (DC) for CAL in acute phase of KD.50 KD children with CAL, 130 KD children without CAL, 30 children with acute upper respiratory infection and 100 healthy children were recruited and indicators reflecting vagal activity including Dc were measstuogram. KD children with cAL showed decreased vagal activity with significantly lower values of DC. DC was negatively correlated with levels of N-terminal pro-brain natriuretic peptide (NT-proBNP) and C-reactive protein (CRP) in KD children. DC was a usable cardiac electrophysiological index to predict cAL in children with KD, with an area under the receiver operating characteristic curve (AUC) of 0.741. The cutoff value of DC for predicting CAL in KD children was 4.37 ms. DC was an independent predictor of CAL in children with KD, evaluated by multiple logistic regression analysis, KD children with Dc ≤ 4.37 ms had an increased risk of CAL, with odds ratios (OR) of 5.94. Our study illustrates DC could be used to predict CAL in acute phase of KD. Kawasaki disease (KD) is an acute febrile systemic vasculitis syndrome, which is one of the most common acquired heart disease in children 1. Coronary artery lesion (CAL) as one of the most serious complications, which could result in coronary artery aneurysm, even myocardial infarction and sudden death, that cause serious damage to children's health, occurs in 25% of untreated children with KD 2-4. Studies have shown that some biochemical indicators are associated with CAL in KD, but there are relatively few reliable indicators for predicting CAL in the acute phase of disease 5-8. Heart rate variability (HRV) reflects beat-to-beat changes in RR intervals, which is a traditional, non-invasive method detecting autonomic nervous function. Root mean squared successive difference (rMSSD), percentage of successive normal sinus RR intervals >50 ms (PNN50) belongs to the time-domain variables of HRV, high frequency (HF) belongs to the frequency domain variable of HRV, low values for these indicators indicate hypoactivity of the vagal nerve 9-11. Decreased vagal activity has been found in patients with coronary artery disease in adults by HRV analysis, which is closely related to the prognosis and the severity of CAL 12-14. Since HRV method cannot accurately distinguish between the vagal and sympathetic activities of the autonomic nervous system, Heart rate deceleration capacity (DC) as a new indicator, which reflects the general trend of sinus rhythm RR interval and its ability to decelerate, has been discovered that can more accurately and quantitatively evaluate vagal activity and has a better warning ability of adverse cardiac events than HRV 15-18. In this study, we aimed to investigate the correlation of vagal activity with CAL in KD children, and assess the predictive value of DC for CAL in acute phase of KD.