In recent years, sodium hypochlorite and chlorhexidine digluconate have been the gold standard of irrigation solutions utilized within the disinfection protocol during root canal treatments. Nowadays, it is known that, during chemical disinfection of the root canal, consecutive application of sodium hypochlorite and chlorhexidine digluconate leads to the formation of an orange-brown precipitate. This precipitate is described as being chemically similar to para-chloroaniline, which is suspected to have cytotoxic and carcinogenic effects. Concerns also exist regarding its influence on the leakage of root canal fillings, coronal restorations, and tooth discoloration. The purpose of this article is to review the literature on the interaction of sodium hypochlorite and chlorhexidine digluconate on the tooth and its surrounding tissues, and to discuss the effect of the precipitate formed during root canal treatment. We further address options to avoid the formation of the precipitate and describe alternative irrigation solutions that should not interact with sodium hypochlorite or chlorhexidine digluconate.