Although hyponatremia frequently occurs in Kawasaki disease (KD), the clinical characteristics of KD patients with hyponatremia and the pathogenesis of hyponatremia in KD remain unknown. The aims of this study were to define the clinical characteristics of KD patients with hyponatremia (serum sodium <135 mEq/l) and to determine the factors associated with its development. One hundred and fourteen patients with KD were included in this study. Fifty-one patients (44.7%) had hyponatremia. Coronary artery lesions and dehydration were significantly more common in patients with hyponatremia. The duration of fever was significantly longer in patients with hyponatremia. Pyuria and hematuria were present significantly more often in patients with hyponatremia. The serum concentrations of potassium, chloride and total cholesterol were significantly lower in patients with hyponatremia. Serum C-reactive protein and alanine aminotransferase were significantly higher in patients with hyponatremia. Some patients with pyuria and hyponatremia exhibited increased excretion of urinary tubular epithelial cells and urinary casts. There was no difference in the incidence of diarrhea between patients with hyponatremia and patients without hyponatremia. These results indicate that hyponatremia in KD occurs in patients exhibiting severe inflammation. Further studies will be necessary to confirm the pathogenic mechanisms of hyponatremia in patients with KD.