The purpose of this study was to evaluate the presence of A. actinomycetemcomitans, P. gingivalis, P. intermedia, E. corrodens and F. nucleatum in 30 subjects with chronic periodontitis treated by scaling and root planing (SRP) plus minocycline (test group) during 12 months with regular trimester maintenance care. Additionally, we evaluated whether the beneficial effects of the therapy on the microbial flora persisted for 24 months. The test group (n = 15) and the control group [SRP plus placebo (n = 15)] were randomly assigned. After SRP, subjects received minocycline or placebo at the baseline, and at 3, 6, and 9 months at all sites with a periodontal pocket depth (PD) of >or= 6 mm. Moreover, two homologous teeth, initially PD >or= 6 mm, were clinically and microbially monitored by PCR at the baseline, and at 3, 6, 9, 12 and 24 months. Differences in mean PD values between groups were analyzed by Student's t-test (P < 0.05). The results for bacterial frequencies showed no significant differences between groups (Fisher's Exact test, P < 0.05) or between time-points (Friedman test, P < 0.05). We failed to detect any differences between groups related to the presence of target pathogens for 12 months. The effects of both therapies on the microbial flora did not persist for 24 months. The group without supportive periodontal therapy showed an improvement in the pattern of pathogens with either of the therapies.