Although an increased level of serum brain natriuretic peptide (BNP) has been reported in children in the acute phase of Kawasaki disease (KD), no precise relation was documented between the serum BNP level and left ventricular (LV) systolic function. We hypothesized that the increased BNP levels may be explained by diastolic abnormalities in those with KD. We prospectively studied 25 patients in the acute phase of KD. Patients with abnormal systolic function were excluded. Pediatric cardiologists making the assessment of LV diastolic function were blinded to the BNP levels. Doppler interrogation was applied to measure LV inflow velocities, which were transformed to z scores using control measurements obtained from 83 healthy subjects. In the patients, the BNP levels ranged from 2.0 to 450.0 pg/ml, with a mean of 54.0 ± 102.8 pg/ml. Six patients with abnormal velocities (> 2 SD in z score) showed significantly higher levels of BNP (152 ± 173 pg/ml) than those in the remaining patients (p < 0.01). The BNP levels correlated positively with diastolic atrial velocity in z score (r = 0.51, p < 0.05), and negatively with diastolic early velocity to atrial velocity ratio in z score (r = -0.75, p < 0.01). This study suggests that LV diastolic dysfunction may occur in some children in the acute phase of KD, causing an increased level of BNP.