BACKGROUND The purpose of this 9-month study was to compare the effect of scaling and root planing alone (control) to that of scaling and root planing plus application of chlorhexidine chips (test). METHODS Twenty-six subjects having two non-adjacent sites in non-molar teeth with probing depth > or =5 mm and bleeding on probing participated in this split-mouth trial. At baseline, the patients received full-mouth scaling and root planing followed by placement of chlorhexidine chips secured by cyanoacrylate at test sites and placement of cyanoacrylate alone at control sites. Test sites still > or =5 mm deep at 3 and 6 months were retreated with renewed chlorhexidine chip application. Recordings of bleeding on probing, probing depths, and clinical attachment levels were performed at baseline, after 6 weeks, and after 3, 6, and 9 months. RESULTS Improvements of bleeding scores, probing depths and clinical attachment levels were observed for both test and control sites at 6 weeks compared to baseline. Subsequently, all three measurements remained comparatively stable throughout the study. No differences in improvements were found comparing test and control sites. CONCLUSIONS This study failed to observe any adjunctive effect of subgingival placement of chlorhexidine chips after scaling and root planing.