Chlorhexidine is one of the commonly used agents in the treatment of periodontitis. In the present study, a biodegradable dental chip of chitosan containing chlorhexidine was evaluated both in vitro and in vivo, as a targeted drug delivery system in patients of chronic periodontitis. Thirty patients having localized periodontal pockets >= 5 mm were selected. At baseline, the experimental patients received full mouth scaling and root planing followed by placement of a chlorhexidine chip. The placebo group received plain chitosan chips, and conventional scaling and root planing were performed for the control group. Measurements of plaque, gingival index were recorded at 1, 2, 3, and 4 months. Probing depth and clinical attachment levels were recorded at the 3rd and 4th month. GCF and saliva samples were procured from the subjects to analyze the drug release at 0, 2, 4, 6, and 24 h and on days 2, 3, 5, 7, 9, 11, 13, 15, 30, 60, and 90. The study showed improvement in plaque index, gingival index, probing depth, Inca clinical attachment levels, but the chlorhexidine chip-treated group showed a significantly better improvement than placebo and control groups at the end of 120 clays. Based on the results of the present in vivo study, we can conclude that the chlorhexidine-containing chitosan drug delivery system may he an adjunct in treating patients with chronic periodontitis. Drug Dev Res 70:395-401, 2009. (C) 2009 Wiley-Liss, Inc.