We compared the use of a rotary electric toothbrush with conventional toothbrushing for their effectiveness in modulating the subgingival microbiota. Forty subjects who had received periodontal treatment for moderate to advanced periodontitis and were on 3-month periodontal maintenance were divided into two equal groups matched for age and sex. One group used only the rotary tooth cleaner and the other group used conventional toothbrushing, dental floss, and toothpicks for 12 months. Subgingival plaque samples (two sites per patient) were taken from 10 subjects per group at baseline, 6 months, and 12 months and analyzed for percentage of obligate anaerobes and colony-forming units of black-pigmented Bacteroides, Fusobacterium, Actinomyces, Streptococcus, and Veillonella spp. The percentage of spirochetes and motile rods was determined by darkfield microscopy. Results showed that levels of obligate anaerobes, Fusobacterium, and Actinomyces and percentage of spirochetes and motile rods decreased significantly (P less than 0.05), while levels of Streptococcus spp. increased (P less than 0.05) for both groups. However, there was no significant difference between the two groups, indicating that the rotary tooth cleaner and conventional toothbrushing are equally effective in controlling gingivitis and fostering a less pathogenic microflora.