The purpose of this study was to investigate the correlation between the composition of bacterial flora from infected root canals and clinical symptoms. The materials evaluated consisted of 28 teeth from 25 patients with apical periodontitis. Eubacterium were found to be significantly related to acute or chronic clinical symptoms and Peptococcus, Peptostreptococcus, and Porphyromonas gingivalis to subacute clinical symptoms. We suggested that Peptococcus, Peptostreptococcus, Eubacterium, Porphyromonas, and Bacteroides were significantly related to percussion pain; Porphyromonas and Bacteroides were significantly related to odor in the infected root canals. Many Bacteroides were isolated from most of the infected root canals.