In an attempt to elucidate the etiology of Kawasaki disease (KD), the microflora of the small intestine was investigated in 15 Japanese KD patients. The range of bacterial species adhering to the lumen of the jejunum of KD patients was quite different from that of controls. A wider variety of bacteria was isolated from jejunal biopsies in the acute phase of KD as compared with those from control children. Gram-positive cocci were isolated from KD patients predominantly. Notably, five kinds of streptococci and two kinds of staphylococci were isolated only from KD patients. Further investigation of the microflora of the small intestine of KD patients may provide clues to clarify the pathogenesis of this disease.