The purpose of the present investigation was to examine the effect of SRP on clinical and microbiological parameters in 57 subjects with adult periodontitis (mean age 47± 11 years). Subjects were monitored clinically and micro-biologically prior to and 3, 6 and 9 months after full-mouth SRP under local anaesthesia. Clinical assessments of plaque, redness, suppuration, BOP, pocket depth and attachment level were made at 6 sites per tooth. The means of duplicate attachment level measurements taken at each visit were used to assess change between visits. Clinical data were averaged within each subject and then averaged across subjects for each visit. Subgingival piaque samples were taken from the mesial aspect of each tooth and the presence and levels of 40 subgingival taxa were determined using whole genomic DNA probes and checkerboard DNA-DNA hybridization. The mean levels and % of sites colonized by each species (prevalence) was computed for each subject at each visit. Differences in clinical and microbiological parameters before and after SRP were sought using the Wilcoxon signed ranks test or the Quade test for more than 2 visits. Overall, there was a mean gain in attachment level of 0.11±0.23 mm (range –0.53 to 0.64 mm) 3 months post-therapy. There was a significant decrease in the % of sites exhibiting gingival redness (68 to 57%) and BOP (58 to 52%) as well as a mean (±SEM) pocket depth (3.3±0.06 to 3.1 ±0.05 mm). Sites with pre-therapy pocket depths of <4 mm showed a non-significant increase in pocket depth and attachment level. 4–6 mm pockets showed a significant decrease in pocket depth and a non-significant gain in attachment post-therapy, while 6 mm pockets showed a significant decrease in pocket depth and attachment level measurements post-therapy. Significant clinical improvements were seen in subjects who had never smoked or were past smokers but not in current smokers. Mean prevalences and levels of P. gangivalis, T. denticola and B. forsythus were significantly reduced after SRP. while A. viscosus showed a significant increase in mean levels. The mean decrease in prevalence of P. gingivalis was similar at all pocket depth categories, while B. forsythus decreased more at shallow and intermediate pockets and A. viscosus increased most at deep sites, P. gingivalis, B. forsythus and T. denticola were equally prevalent among current, past and never smokers pre-therapy, decreased significantly post-SRP in never and past smokers but increased in current smokers. Clinical improvement post-SRP was accompanied by a modest change in the subgingival microbiota, primarily a reduction in P. gingivalis, B. forsythus and T. denticola, suggesting potential targets for therapy and indicating that radical alterations in the subgingival microbiota may not be necessary or desirable in many patients.