In periodontitis lesions with interproximal craters, periodontal flap surgery with osseous recontouring allows more apical positioning of the soft periodontal tissue than flap surgery without osseous recontouring. The present study determined the clinical and microbiologic responses to periodontal surgery with and without osseous recontouring in adult periodontitis lesions with interproximal craters. In 7 osseous surgery patients, osteoplasty and ostectomy were performed from the lingual/palatal aspect to eliminate interproximal osseous defects and to partly mimic the original alveolar bony transition to neighboring teeth. In 7 nonosseous surgery patients, the surgical flap was adapted to the preexisting osseous level. Clinical monitoring included periodontal probing depth, Plaque Index, gingival bleeding index, and radiographic examination. Samples of the subgingival microbiota were examined. In sites treated with osseous surgery, mean pocket depth was 5.5 mm at baseline, 1.9 mm at 1 month, 2.0 mm at 3 months, and 2.1 mm at 6 months. In sites not receiving osseous recontouring surgery, the corresponding pocket depths were 5.9 mm, 3.1 mm, 3.8 mm, and 4.1 mm. At baseline in the osseous surgery group, Actinobacillus actinomycetemcomitans was recovered from one patient and Porphyromonas gingivalis from 5 patients; posttreatment, these microbiota were not detected in any patient. In the nonosseous surgery group, the presence of A actinomycetemcomitans increased posttreatment, and levels of P gingivalis remained essentially unchanged after therapy. This study suggests that in patients not receiving adjunctive antibiotic therapy, apically positioned flap surgery with osseous recontouring is more effective than apically positioned flap surgery without osseous recontouring in reducing periodontal pocket depth and levels of major periodontal pathogens.