Chemical auxiliary substances (CAS) are essential for a successful disinfection and cleanness of the root canals, being used during the instrumentation and if necessary, as antimicrobial intracanal medicaments. Different CAS have been proposed and used, among which sodium hypochlorite (NaOCl), chlorhexidine (CHX), 17% EDTA, citric acid, MTAD and 37% phosphoric acid solution. CHX has been used in Endodontics as an irrigating substance or intracanal medicament, as it possesses a wide range of antimicrobial activity, substantivity (residual antimicrobial activity), lower cytotoxicity than NaOCl whilst demonstrating efficient clinical performance, lubricating properties, rheological action (present in the gel presentation, keeping the debris in suspension); it inhibits metalloproteinase, is chemically stable, does not stain cloths, it is odorless, water soluble, among other properties. CHX has been recommended as an alternative to NaOCl, especially in cases of open apex, root resorption, foramen enlargement and root perforation, due to its biocompatibility, or in cases of allergy related to bleaching solutions. The aim of this paper is to review CHX's general use in the medical field and in dentistry; its chemical structure, presentation form and storage; mechanism of action; antimicrobial activity including substantivity, effects on biofilms and endotoxins, effects on coronal and apical microbial microleakage; tissue dissolution ability; interaction with endodontic irrigants; effects on dentin bonding, metalloproteinases and collagen fibrils; its use as intracanal medicament and diffusion into the dentinal tubules; its use as disinfectant agent of obturation cones; other uses in the endodontic therapy; and possible adverse effects, cytotoxicity and genotoxicity.