BACKGROUND: The present investigation examined clinical and microbial changes after a combined aggressive antimicrobial therapy in subjects identified as "refractory" to conventional periodontal therapy. METHOD: Fourteen subjects were identified as "refractory" based on full-mouth mean attachment loss and/or >3 sites with attachment loss > or =3 mm following scaling and root planing (SRP), periodontal surgery and systemic antibiotics. After baseline monitoring, subjects received SRP, locally delivered tetracycline at pockets > or =4 mm, systemically administered amoxicillin (500 mg, t.i.d. for 14 days)+metronidazole (250 mg, t.i.d. for 14 days) and professional removal of supragingival plaque weekly for 3 months. Subjects were monitored clinically every 3 months post-therapy for 2 years. Subgingival plaque samples were taken at the same time points from the mesial aspect of each tooth and the levels of 40 subgingival taxa were determined using checkerboard DNA-DNA hybridization. Mean levels of each species were averaged within a subject at each visit. Significance of changes in clinical and microbiological parameters over time were evaluated using the Friedman or Wilcoxon signed ranks test. RESULTS: On average, subjects showed significant improvements in all clinical parameters after therapy. Mean (+/-SEM) full-mouth pocket depth reduction was 0.83+/-0.13 mm and mean attachment level "gain" was 0.44+/-0.12 at 24 months. Clinical improvement was accompanied by major reductions in multiple subgingival species during the first 3 months of active therapy that were maintained for most species to the last monitoring visit. Reductions occurred for three Actinomyces species, "orange complex" species including Campylobacter showae, Eubacterium nodatum, three Fusobacterium nucleatum subspecies, Peptostreptococcus micros, Prevotella intermedia as well as the "Streptococcus milleri" group, Streptococcus anginosus, Streptococcus constellatus and Streptococcus intermedus. Subjects differed in their response to therapy; six modest response subjects exhibited less attachment level gain and were characterized by reductions in the microbiota from baseline to 3 months, but re-growth of many species thereafter. CONCLUSIONS: The combined antibacterial therapy was successful in controlling disease progression in 14 "refractory" periodontitis subjects for 2 years.