The purpose of this study was to evaluate, on a short-term basis, the clinical and microbiological effects of a single course of scaling and root planing as compared with those obtained by flap surgery in patients with moderate to advanced periodontitis. 11 patients participated in the study. Using a split-mouth design, one quadrant of the mouth was treated with reverse bevel flap surgery, whereas the contralateral one was subjected to a single course of scaling and root planing. 2 approximal sites on single-rooted teeth with a pocket depth greater than or equal to 5 mm were monitored clinically and microbiologically for 16 weeks after active treatment. Both techniques resulted in a gain of probable attachment levels, a reduction in bleeding on probing and a reduced mean pocket depth, although 31.2% of the sites in the scaling and root planing group still had 6-7 mm deep pockets at 8 and 16 weeks after treatment. Both techniques reduced median relative proportions and frequencies of detection of black-pigmented Bacteroides species. A highly statistically significant increase (p less than 0.01) in median proportions of oral streptococci was recorded only for surgery within the 1st month post-operatively. No correlation was found between residual pocket depth and any of the microbiological parameters considered in the study, suggesting that residual pocket depth does not exert a significant influence on bacterial subgingival recolonization after therapy. The results from this study suggest that surgery can be as effective as scaling and root planing in favoring the establishment of micro-organisms compatible with periodontal health, although this effect is limited to the 1st month after therapy.