The present study is focused on a new type of biocompatible hydrogels based on natural polymers (chitosan and pectin) which are designed to deliver the drug into the periodontal pocket. The hydrogels preparation method was complex coacervation. Infrared spectroscopy was employed to confirme the interpolymeric complex formation between the amino groups of chitosan and the carbonyl groups of pectin. Hydrogels presented a good Chlorhexidine loading and release capacity. In vitro release of Chlorhexidine and the swelling degree experiments were carried out in conditions mimicking the oral environment. The cytotoxicity of these materials was investigated on human dermal fibroblasts.