The microbial flora from 46 adult periodontitis lesions of 23 patients and 18 sites in 9 healthy persons were examined and levels of serum IgG antibody to gram negative periodontal disease-associated bacteria were measured by enzyme-linked immunosorbent assay. Plaque samples and serum samples were taken 40-50 days after initial preparation consisting of scaling and root planing. To evaluate the effects of the therapy on 10 patients with adult periodontitis, changes in clinical parameters were compared with alterations of the microbial flora and serum IgG antibody levels. Black-pigmented Bacteroides species, mainly Bacteroides gingivalis, were found to be predominant in periodontitis lesions. A significant relationship was found between the prevalence of B. gingivalis and elevated titers of serum IgG antibody against the microorganism. No relationships between Bacteroides intermedius, Actinobacillus actinomycetemcomitans and elevated titers of serum IgG antibody to them were detected. The fact that there was no marked reduction of serum IgG antibody to B. gingivalis after initial preparation suggests that a more extended, longitudinal study is required. Although brushing resulted in a significant reduction of the number of total cultivable organisms in samples from periodontal pockets, no significant proportional changes in gram-negative bacteria in the lesional flora were found. Initial preparation was not effective in eliminating gram-negative bacteria from deep periodontal pockets. However, the microbiological shifts, especially the reduction in the proportion and frequency of detection of B. gingivalis in periodontal pockets, was paralleled by significant improvement in the clinical parameters.