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Endodontic restorations often fail due to inadequate disinfection of the root canal even though the antimicrobial irrigants used have been shown to be capable of killing the bacterium frequently implicated in this complication, Enterococcus faecalis (Ef). Extracted human teeth were root-prepared and filled with a liquid culture of Ef. Following incubation, the root canals were irrigated with 1% sodium hypochlorite (NaOCl), electrochemically activated water or saline control. Irrigation was modelled using an electronic pipette to deliver the solutions at a reproducible flow velocity. A series of parallel experiments employed a membrane biofilm model that was directly immersed into irrigant. Experimental conditions where contiguous between the extracted tooth model and biofilm model wherever possible. After 60 s of exposure, 1% NaOCl effectively sterilised the biofilm model, whereas log 3.36 viable Ef where recoverable from the analogous extracted tooth model, the other irrigants proved ineffective. Biofilms of Ef were susceptible to concentrations of irrigant that proved ineffective in the tooth model. NaOCl was the most effective biocide in either case. This suggests that the biofilm modality of bacterial growth may not be the most important factor for the recalcitrance of root canal infections during endodontic irrigation; it is more likely due to the inability of the irrigant to access the infection.