In the pathophysiology of inflammatory bowel diseases (IBD), interaction between mucosal immune system and commensal enteric bacteria plays an important role. In this study, we performed terminal restriction fragment length polymorphism (T-RFLP) analyses of fecal microbiota from five siblings, which included two subjects with ulcerative colitis (UC). Fecal microbiota in the two siblings with UC were clearly different from those obtained from the healthy siblings. The mother's pattern was a cross between the UC and the healthy siblings. Predicted bacteria based on a BslI-digested T-RFLP database showed a tendency of increases in Clostridium cluster IX and decreases in Clostridium cluster XIVa in the UC siblings. These data indicate that fecal microbial communities differed between UC subjects and healthy individuals under conditions where environmental effects on fecal microbiota may be minimized.