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The purpose of this study was to develop sustained release systems based on chitosan (CS) and montmorillonite (MMT) for chlorhexidine (CLX). Nanocomposites were prepared by ion-exchange. CLX systems were characterized by X-ray powder diffraction (XRD), thermal analysis (TGA), Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM) and X-ray fluorescence analysis (XRF). The mucoadhesion properties of CLX nanocomposites were evaluated by SEM. The release behavior of these systems was also studied by the dialysis technique. The antibacterial activity was investigated in vitro by the disk diffusion test. Results showed long-term sustained release of CLX from the hybrid carriers without initial burst release. The release profiles of CLX from the carriers suggested the diffusion through a swollen matrix and water filled pores as the controlled drug release mechanism. The CLX hybrid nanosystem containing the positively-charged chitosan exhibited good mucoadhesion properties maintaining the CLX antimicrobial properties.