Background Chlorhexidine (CHX) rinsing after periodontal surgery is common. We assessed the clinical and microbiological effects of two CHX concentrations following periodontal surgery. Materials and methods In a randomized, controlled clinical trial, 45 subjects were assigned to 4 weeks rinsing with a 0.05 CHX/herbal extract combination (test) or a 0.1% CHX solution. Clinical and staining effects were studied. Subgingival bacteria were assessed using the DNA-DNA checkerboard. Statistics included parametric and non-parametric tests (p < 0001 to declare significance at 80% power). Results At weeks 4 and 12, more staining was found in the control group (p < 0.05 and p < 0.001, respectively). A higher risk for staining was found in the control group (crude OR: 2.3:1, 95% CI: 1.3 to 4.4, p < 0.01). The absolute staining reduction in the test group was 21.1% (9 5% CI: 9.4-32.8%). Probing pocket depth (PPD) decreases were significant (p < 0.001) in both groups and similar (p=0.92). No rinse group differences in changes of bacterial counts for any species were found between baseline and week 12. Conclusions The test CHX rinse resulted in less tooth staining. At the study endpoint, similar and high counts of periodontal pathogens were found.