In the treatment of intracanal and periodontal infections, the local application of antibiotics and other therapeutic agents in the root canal or in periodontal pockets may be a promising approach to achieve sustained drug release, high antimicrobial activity and low systemic side effects. Microparticles made from biodegradable polymers have been reported to be an effective means of delivering antibacterial drugs in endodontic and periodontal therapy. The aim of this review article is to assess recent therapeutic strategies in which biocompatible microparticles are used for effective management of periodontal and endodontic diseases. In vitro and in vivo studies that have investigated the biocompatibility or efficacy of certain microparticle formulations and devices are presented. Future directions in the application of microencapsulation techniques in endodontic and periodontal therapies are discussed.