The effect of hand or ultrasonic instrumentation on the subgingival microflora of periodontal pockets was investigated. Pockets with probing depths of 6-9 mm were selected in 12 patients and were randomly assigned per patient to the experimental and control groups. After oral hygiene instruction, instrumentation of the experimental pockets was carried out either by ultrasonic or by hand instruments in a split-mouth design. The treatment effect on the subgingival microbiota was evaluated by microscopic and culture studies of subgingival plaque samples, while in addition, supragingival plaque, bleeding after probing and probing pocket depth were scored. Examinations were carried out before and 7, 21 and 49 days after treatment. The hand and ultrasonic treatments were equally effective in reducing probing pocket depths and bleeding scores. At the end of the experimental period, the probing depths of 54% of the hand-treated pockets and 43% of the ultrasonic-treated pockets were reduced to 4 mm or less while the bleeding scores were reduced to 29% and 22%, respectively. The analysis of microscopical and cultural data did not show any differences between hand and ultrasonic debridement. Both treatments reduced the microscopical counts of rods, spirochetes and motiles and reduced the total colony-forming units and number of black-pigmented Bacteroides and Capnocytophaga, resulting in a subgingival microbiota consistent with periodontal health.