Successful treatment of apical periodontitis is dependent on the elimination of the infective microflora from the necrotic root canal system. Antimicrobial irrigating solutions and other locally used disinfecting agents and medicaments have a key role in the eradication of the microbes. While most if not all presently used disinfecting agents rapidly kill even the resistant microbes when tested in vitro in a test tube, the effectiveness of the same agents is clearly weaker in the in vivo conditions. Recent studies have given valuable information about the interaction of endodontic disinfecting agents with dentin and other compounds present in the necrotic root canal. As a result of such interactions the antimicrobial effectiveness of several of our key disinfectants may be weakened, or even eliminated under certain circumstances. Different disinfectants show different sensitivity to the action by the various potential inactivators, such as dentin, serum proteins, hydroxyapatite, collagen derived from different sources, and microbial biomass. This review is a summary of our present knowledge of the mostly negative interactions between endodontic disinfecting agents and the various compounds present in the root canal environment.