The clinical and microbiological effects of once daily subgingival irrigations with 1 ml of 0.2% chlorhexidine gluconate (CH) during 14 days were evaluated in 23 patients with 4 to 6 mm contralateral pockets. On Days 0, 14 and 28, evaluations were made of the plaque index, the gingival index, gingival bleeding on probing pocket depth and of microbiological variables (phase-contrast microscopy). Supragingival scaling was carried out but no oral hygiene instructions were given to patients at the start of the trial. Twenty-three test sites (subgingival CH) and 23 control sites (subgingival distilled water + supragingival CH) were studied. The clinical results showed a significant reduction of the gingival index (P less than 0.05) in the test group with respect to the control group on Day 14. No other clinically significant differences could be observed in the test group with respect to the control group. A significant reduction in the proportions of spirochetes (P less than 0.05) and a significant increase in the proportions of cocci (P less than 0.005) were observed in the test group on Day 14. CH irrigation as a subgingival monotherapy yielded transient microbiological and limited clinical effects.