The aim of root canal treatment is to eliminate bacteria from the infected root canal and to prevent reinfection. Biomechanical cleaning and shaping greatly reduces the number of bacteria. Nevertheless, due to anatomical complexity of the root canal system, residues and bacteria cannot be removed completely. Therefore, various substances have been used during canal preparation to remove debris, necrotic tissue, bacteria and smear layer. The most common irrigant of choice is sodium hypochlorite (NaOCI): it is an effective antimicrobial agent and tissue solvent. However, NaOCI can be toxic. Chlorhexidine gluconate (CHX) is a broad-spectrum antimicrobial agent. As a root canal irrigant and intracanal medicament, CHX has an antibacterial efficacy comparable to that of NaOCI, and is effective against resistant bacterial strains. CHX may result in residual antimicrobial activity of the dentine surface after prolonged exposure of the root canal to CHX. CHX also has a low grade of toxicity. In this review CHX will be discussed in detail.