The effects of ultrasonic and sonic scalers on the subgingival microflora were investigated in vitro and in vivo. In the in vitro investigation, 27 plaque samples collected from periodontal pockets were submitted to ultrasonic and sonic vibrations for 10, 30 and 60 s. Bacterial suspensions were examined by darkfield microscopy to detect qualitative changes and cultured to evaluate the total number of cultivable bacteria. Microscopic counts following both instrumentations showed a decrease in the proportions of spirochetes and motile rods and an increase in the % of coccoids and rods. The changes were directly related to the time-period of instrumentation. Comparison between both types of instrumentation showed significant differences and more pronounced changes were observed with the ultrasonic than the sonic scaler. Spirochetes and motile rods were reduced to approximately 0.1% after ultrasonic treatment versus 24.7% after sonic instrumentation. Cultural observations showed a marked increase in total number of colony-forming units following both treatments. The clinical investigation included 66 periodontal pockets which were instrumented subgingivally for 10 and 30 s with ultrasonic or sonic scalers. Qualitative changes were similar to those observed in vitro, i.e., reduction in spirochete and motile rod counts as well as the other morphotypes with an increase in coccoid cells. Total counts of bacteria were reduced following debridement. No difference in the microscopic or cultural data was found between ultrasonic and sonic instrumentation.