Microbes and their by-products play a decisive role in the pathogenesis of pulp and periapical disease. The goals of an endodontic treatment are therefore the elimination of microorganisms and microbial components from the root canal system, and prevention of its re-infection.

Instrumentation and irrigation is widely recommended in order to achieve chemomechanical debridement, because instrumentation alone can not remove pulp tissue or microorganisms completely from the root canal system due to its complexity, leaving up to half of the canal surface untouched following instrumentation, cleaning and disinfection rely on irrigation.