In an examiner blind positive/negative controlled 6-month study, the efficacy of supragingival irrigation with 0.06% chlorhexidine gluconate on the marginal and subgingival microflora in naturally occurring gingivitis was evaluated. The 222 patients enrolled in the study were assigned to one of four groups: Group 1: Once daily irrigation with 300 ml water followed by irrigation with 200 ml 0.06% chlorhexidine gluconate (experimental); Group 2: Twice daily rinsing with 15 ml 0.12% chlorhexidine (positive control); Group 3: Once daily irrigation with 500 ml water (irrigation control) and Group 4: Sodium fluoride dentifrice for normal oral hygiene only (negative control). All groups received the same sodium fluoride dentifrice for tooth brushing. All patients received a supra- and subgingival oral prophylaxis after baseline examination and at the end of the investigation. Plaque samples were analyzed from 105 patients at baseline, 93 patients at 3 months and 88 patients at 6 months. The 6-months results demonstrated that, when compared with tooth brushing alone, adjunctive supragingival irrigation with 0.06% chlorhexidine gluconate was most effective by significantly reducing (P less than or equal to 0.008) both log10 CFU and % of Gram-negative anaerobic rods and black-pigmented Bacteroides. Chlorhexidine rinse also significantly (P less than or equal to 0.008) reduced log10 CFU of black-pigmented Bacteroides at 6 months. Both chlorhexidine regimens significantly (P less than or equal to 0.008) increased the % of Gram-positive facultative cocci compared to water irrigation at 3 months. Water irrigation had a limited effect on any of the assessed bacterial groups (log10 CFU and %).(ABSTRACT TRUNCATED AT 250 WORDS)