This double-blind study used a split-mouth design to investigate the microbiological and clinical effects of 0.2% chlorhexidine enclosed in fixtures. Twelve patients had 46 fixtures implanted. At second-stage surgery, a microbiological sample (baseline sample) of the inner parts of the fixtures was taken. Then, a 0.2% chlorhexidine solution was applied into the inner space of 23 fixtures (test group), and in 23 fixtures saline was applied (control group). Abutments were installed and gingival index, plaque index and crevicular fluid flow were monitored weekly. After 6 weeks, a second microbiological sample of the inner part of the fixtures was taken. At baseline, viable bacteria were detected within 46% of the fixtures. After weeks, bacteria were found in 87% of the fixtures. The numbers of bacteria in the control group were significantly higher than those in the test group. The results indicate that, after first-stage surgery, contamination of the inner spaces of the fixtures is commonplace. Application of a 0.2% chlorhexidine solution at second-stage surgery inhibits growth or acquisition of bacteria in the fixtures. In both test and control groups, the crevicular fluid flow as well as the gingival index decreased during the experimental period. At 4, 5, and 6 weeks after chlorhexidine application, these values in the test group appeared lower, but did not attain statistical significance.