The aim of this study was to explore the microbiological and clinical effects of an antiseptic dental varnish when applied to periodontally diseased teeth after mechanical therapy. 20 subjects participated in this placebo controlled, double blind prospective longitudinal study. 2 experimental sites with a pocket probing depth > or =5 mm were chosen in each subject. The control varnish, consisting of ethanol, ethylacetate and polyvinylbutyral, was applied to one of the selected teeth and the test varnish, containing 1% chlorhexidine and 1% thymol in addition, was applied to the other one. Clinical parameters were assessed, and microbiological samples were obtained from the two study sites at baseline (6-10 weeks after completion of conventional periodontal therapy), and 2, 4 and 12 weeks thereafter. The mean PLI at baseline was very low and, therefore, only a minimal potential for a further improvement existed. During the 12-week observation period, the mean PLI increased significantly at sites treated with the placebo varnish, while no similar trend for an increase in PLI was detected in the test sites. The bleeding tendency seemed to remain unaffected by the application of the varnish. On the microbiological level, no relevant differences could be detected between placebo and test sites at baseline, or during the follow-up period. In conclusion, the application of a dental varnish with antimicrobial properties after mechanical periodontal therapy had little effect in subjects with good oral hygiene.