The short-term bactericidal effect of 2% chlorhexidine gel, 4% stannous fluoride gel or amine fluoride gel containing 1.25% fluoride on the subgingival microflora was determined in 40 periodontal pockets of 10 patients. The antimicrobial gels or placebo gel were applied in 5-9 mm deep periodontal pockets 3 times within 10 min. Before and 30 min after the applications, samples were taken of the subgingival microflora for determination of the total number of bacteria as well as the number of black pigmented Bacteroides. Reductions of the total number of bacteria were found in all test groups. The reductions found in the pockets treated with chlorhexidine gel or stannous fluoride gel were significantly greater than the reduction found in the pockets treated with a placebo gel. A significant reduction of black-pigmented Bacteroides was found after treatment with chlorhexidine gel or amine fluoride gel. It is concluded that 2% chlorhexidine gel or 4% stannous fluoride gel has a more than 99% reduction effect on the microflora of periodontal pockets within 30 min after application.