The successful treatment of the root canal requires the elimination of pulp tissue and bacteria and the alteration of its environment to prevent further colonization. The root canal irrigation is the introduction of chemicals for antimicrobial activity, demineralization, tissue dissolution, bleaching, deodorizing, and hemorrhage control through a flushing mechanism. Several irrigating solutions have cytotoxic potential, and they may cause damage if they gain access into the periapical tissues, high concentration can also cause erosion on the canal dentinal walls. The disinfection of the root canal system is challenging due to the complex internal anatomy and dentin composition, mechanical preparation cannot achieve the complete removal of pulp tissue and bacteria, and current irrigants cannot accomplish all the tasks required; a detailed understanding of the mode of action of various solutions is essential for optimal irrigation. We will discuss new developments on broad antimicrobial agents against bacteria and fungi typical of the root canal infection without cytotoxicity and mechanical devices for safe and adequate irrigation.