BACKGROUND Although scaling and root planing are considered the therapeutic standard for periodontitis, weakly responding sites often occur. To improve treatment outcome, several chemomechanical treatment concepts have been developed. Recently, the clinical surplus value of a highly concentrated chlorhexidine varnish has been shown when used as an adjunct to sequential scaling and root planing. The aim of this study was to explore the clinical effects of a treatment strategy for chronic periodontitis based on a combination of same-day full-mouth root planing and subgingival chlorhexidine varnish administration. METHODS A randomized, controlled, single-blind, parallel trial was conducted on 12 chronic periodontitis patients. The control group received oral hygiene instructions and same-day full-mouth root planing. The test group received the same instructions and treatment; however, all pockets were additionally disinfected using a chlorhexidine varnish. Clinical response parameters were recorded at baseline and subsequently after 1 and 3 months. RESULTS Both treatment strategies showed significant reductions in probing depth at both follow-up visits in comparison with baseline levels (P <or=0.029). Yet, at 3 months, initially diseased sites of the test group showed significant additional pocket reductions between 0.70 and 1.37 mm (P <or=0.021). Furthermore, a significant additive clinical attachment gain of 1.17 mm (P = 0.049) for initially deep pockets (>or=7 mm) was found favoring the test group. CONCLUSIONS These preliminary findings suggest that the outcome of same-day full-mouth root planing may benefit from the subgingival administration of a highly concentrated chlorhexidine varnish.