The purpose of this investigation was to examine the short-term effect of apically repositioned flap surgery on clinical and microbiologic parameters in patients with adult periodontitis. A total of 11 patients with moderate to advanced periodontitis received apically repositioned flap surgery. Subjects were monitored during a 3-month pretreatment phase, the baseline surgical phase, and for 3 months postsurgery. Clinical assessments including plaque accumulation, gingival redness, suppuration, bleeding on probing, pocket depth, and attachment level were made at 6 sites per tooth. Subgingival plaque samples were taken from the mesial aspect of each tooth and the presence and levels of 29 subgingival taxa were determined using whole genomic DNA probes and checkerboard DNA-DNA hybridization. The mean levels and percentage of sites colonized by each species (prevalence) were computed for each subject at each visit. After surgery, there was a significant decrease in mean pocket depth and percentage of sites exhibiting gingival redness. Significant decreases were seen in the percentage of sites that had attachment levels 4 mm, with a significant increase in the percentage of sites with attachment levels of 4 to 6 mm after therapy. The mean total DNA probe count for all bacterial species was significantly decreased by both scaling and root planing and surgical therapy. P gingivalis and B forsythus, 2 bacteria previously shown to be susceptible to mechanical therapy, exhibited statistically significant decreases in mean total DNA probe count. Because surgical therapy decreased levels of the suspected periodontal pathogens C rectus, P nigrescens, and C gracilis, it may be speculated that there was a potential added beneficial effect of surgery on the periodontal microbiota.