To identify the origin of urinary leukocytes in Kawasaki disease (KD) patients with pyuria, we prospectively studied clinical and laboratory findings of 23 KD patients. Patients were divided into three groups: patients without pyuria, patients with pyuria in both voided urine and bladder urine obtained by transurethral catheterization (bladder pyuria) and patients with pyuria only in voided urine (urethral pyuria). Pyuria in voided urine was found in ten of 23 KD patients (43.5%), with subsequent urine cultures proving sterile. Five out of ten patients with pyuria in voided urine also exhibited pyuria in bladder urine, whilst the remaining patients did not have pyuria in bladder urine. Urinary protein levels were higher in patients with bladder pyuria and in patients with urethral pyuria than in patients without pyuria. Urinary β2-microglobulin concentrations and serum blood urea nitrogen (BUN) and creatinine levels were higher in patients with bladder pyuria than in patients with urethral pyuria or in patients without pyuria, although the serum BUN and creatinine levels of patients with bladder pyuria were within the normal ranges. These results suggest that some patients with KD develop sterile pyuria that originates from the urethra and/or the kidney as a result of mild and subclinical renal injury.