Introduction: Bacteria are the most common pathogens responsible for pulpal necrosis and periapical disease conditions. The importance of eradicating bacteria and their endotoxic by-products has been highlighted in numerous studies. Aim: The aim of this in vitro study was to establish the efficacy of six endodontic disinfection protocols in eradicating Enterococcus faecalis from single root canals of human teeth. Materials and Methods: Endodontic access cavities were prepared on 86, extracted, single rooted, human teeth. Root canal preparation was done using nickel titanium rotary files. Each tooth was sterilised, inoculated with E. faecalis and randomly allocated to one of seven groups (n = 12). The six disinfection protocols were 3% sodium hypochlorite solution (NaOCl), 2% chlorhexidine digluconate solution (CHX), Chlor-XTRA, 3% NaOCl combined with 2% CHX, 3% NaOCl followed by photo-activated disinfection (PAD) and PAD alone. The seventh group was irrigated with sterile water (control). The roots were fractured longitudinally. Dentine samples from coronal, middle and apical sections of one half of each root were plated onto brain heart infusion (BHI) plates. These were incubated anaerobically at 37⁰C for five days. The colony-forming units (cfu) were counted. The second half of each root was prepared for Scanning Electron Microscopy. The Pairwise Wilcoxon Rank Sum test and the Kruskal-Wallis test were used to compare the cfu counts of the seven groups to one another. Results: Two per cent CHX, Chlor-XTRA, combination of 3% NaOCl and 2% CHX and irrigation with 3% NaOCl followed by PAD were able to eradicate E. faecalis from the coronal levels of the root canals. A combination of 3% NaOCl and 2% CHX and irrigation with 3% NaOCl followed by PAD were able to eradicate E. faecalis from the middle levels of the root canals. None of the disinfection protocols were able to eradicate E. faecalis from the apical levels of all root canals. The regimen of 3% NaOCl followed by 2% CHX was slightly more efficient in eradicating E. faecalis from the root canals than the other disinfection regimens. Dentine erosion and precipitate formation were two incidental observations in some of the samples upon SEM examination.