The purpose of this study was to assess the recolonization of the subgingival microflora following scaling and root planing on single and multiroot teeth with periodontal pockets which were above 5mm. 7 patients with deep pockets were selected for this study. They had not taken antibiotics for 6 months and no history of dental treatment for 6 months before the study. After initial clinical(plaque index, gingival index, probing pocket depth), microbiological and BANA test were determined, each subject received a single session of scaling and root planing, but they were not received oral hygiene instructions. Clinical indices, microbial parameters and BANA test were reassessed 1, 2, and 4 weeks after treatment. The results were as follows : 1. Plaue index, gingival index and pocket depth were not significantly when compared single root group with multiroot group, both groups were siginficantly reduced at 2weeks in plaque index and 2, 4 weeks in gingival index(P<0.05), probing pocket depth was siginificantly changed at 2, 4weeks in multiroot teeth group and 4 weeks in single root teeth group(P<0.05). 2. Percentage of cocci was significantly increased at 4weeks in single root teeth group(P<0.05), motile rod was significantly changed at 4weeks in both group(P<0.05), spirochetes and nonmotile rods were not significantly changed. 3. BANA test was significantly reduced at 1 and 2 weeks (P<0.05) in single root teeth group, multiroot teeth group was not significantly all weeks. This results were suggested that clinical and microbiological effect following scaling and root planing on periodontal disease.