The presence of bacteria in 17 single-rooted teeth, with periapical lesions, was studied throughout a whole period of treatment. The root canals were irrigated with physiologic saline solution during instrumentation. No antibacterial solutions or dressings were used. Bacteria were found in all initial specimens from the teeth (median number of bacterial cells 4 x 10(5), range 10(2) - 10(7)) and the number of strains in the specimens ranged from 1 to 10.88% of the strains were anaerobic. The most commonly isolated species were: Peptostreptococcus micros, Peptostreptococcus anaerobius, Fusobacterium nucleatum, Bacteroides oralis, Bacteroides melaninogenicus subsp intermedius and Eubacterium alactolyticum. Mechanical instrumentation reduced the number of bacteria considerably. Specimens taken at the beginning of each appointment usually contained 10(4) - 10(6) bacterial cells and at the end 10(2) - 10(3) fewer. Bacteria were eliminated from the root canals of eight teeth during the treatment. In seven root canals bacteria persisted despite treatment on five successive occasions. There was no evidence that specific microorganisms were implicated in these persistent infections. Teeth where the infection persisted despite being treated five times were those with a high number of bacteria in the initial sample.