The antimicrobial effect of stannous fluoride (SnF2) on suspected pathogenic morphotypes of bacterial plaque in chronic periodontal disease was assessed. Alterations in morphological groups of subgingival and supragingival plaque bacteria from three diseased sites and one periodontally healthy site were determined by darkfield microscopy in 10 male patients with advanced periodontitis. In addition, clinical indices were also measured. The three diseased sites received either 1.64% SnF2, 0.4% SnF2 or sterile saline by subgingival irrigation. The healthy site received sterile saline only. The patients were seen weekly over a 10-week period and at each appointment bacterial sampling and clinical indices were measured. Results indicated that 1.64% SnF2 caused a dramatic and sustained decrease of subgingival motile bacteria and spirochetes following irrigation. By the sixth week these bacteria returned to 50% of their original concentration. Bleeding index scores, which were significantly reduced, correlated positively to the reduction in motile bacteria and spirochetes. Sites irrigated with 0.4% SnF2 also demonstrated a similar pattern of reduction of motile bacteria and spirochetes but without their total elimination and a more rapid return to original levels. In the diseased sites receiving sterile saline there was a decrease in motile bacteria and spirochetes, corresponding with saline irrigation, which rapidly returned to baseline levels. The healthy control sites were unchanged. Supragingival plaque index scores did not correlate with the bleeding index, motile bacteria and spirochetes, or with subgingival irrigation.