The purpose of this investigation was to examine the clinical and microbiologic effects of apically repositioned flap surgery. Eighteen patients with chronic periodontitis received initial preparation (IP) including scaling and root planing, followed at 3 months by apically repositioned flap surgery at sites with pocket depth > 4 mm. Subjects were monitored clinically and microbiologically at baseline, 3 months after IP, and at 3, 6, 9, and 12 months postsurgery. Clinical assessments of plaque accumulation, gingival redness, suppuration, bleeding on probing, pocket depth, and attachment level were made at six sites per tooth. Subgingival plaque samples were taken from the mesial aspect of each tooth, and the presence and levels of 40 subgingival taxa were determined using checkerboard DNA-DNA hybridization. Significant reductions were seen in mean pocket depth and percentage of sites exhibiting gingival redness and bleeding on probing in both sites that received IP only and in sites receiving IP followed by surgery. Mean attachment level increased significantly for both sets of sites, but the increase was greater at the surgically treated sites. The total DNA probe counts were significantly reduced at sites in both treatment groups. At surgically treated sites, 19 of 40 taxa were significantly reduced posttherapy. At sites receiving IP only, 16 species were significantly reduced over time. While there were some reductions in mean counts after IP in this site group, the major reductions occurred after the surgical phase in these patients, even though these particular sites did not receive surgical therapy. The reduction in pocket depth by surgical means and the associated decrease in reservoirs of periodontal pathogens may be important in achieving sustained periodontal stability.