The aim of the present trial was to study if carefully practiced supragingival plaque control influenced the subgingival microbiota at periodontal sites with suprabony, infrabony, or furcation pockets. 12 subjects, 5 males and 7 females aged 44 to 69 years (mean age 55 years) participated in the study. None of the participants had during the last 12 months received periodontal therapy, and none of the subjects had used antibiotics during a 3-month period preceding the study. Following a screening examination, 6 to 8 sites per subject were selected which had a probing depth of > or = 5 mm. Among these sites, 1-3 sites had a suprabony location, 1-3 sites had an infrabony location, and 1-3 sites were associated with a furcation defect. The selected sites were exposed to a baseline examination at which the following parameters were recorded: plaque, gingivitis, probing pocket depth and probing attachment level. A bacterial sample was obtained from each of the selected sites: 2 sterile paper points were inserted into the pocket and kept in place for 30 seconds. The paper point samples were removed, placed in a vial containing an anaerobically prepared transport medium, and processed using routine procedures. Following the baseline examination, each subject was given a case presentation, received thorough supragingival scaling and was instructed to practice proper plaque control with the use of toothbrush and dentifrice. During the subsequent 30 weeks they were recalled 2-3xper week for professional tooth cleaning. Each session was handled by a dental hygienist and required about 15 min. Re-examinations were performed after 30 weeks. The findings indicated that professionally delivered and frequently repeated supragingival tooth cleaning, combined with careful self-performed plaque control had a marked effect on the subgingival microbiota of moderate to deep periodontal pockets. Thus, at sites with suprabony and infrabony pockets, as well as at furcation sites, the meticulous and prolonged supragingival plaque removal reduced the total number of microorganisms that could be harvested, as well as the % of sites with P. gingivalis.