Objectives: Enterococci faecalis is a pathogenic bacteria strongly associated with endodontic infections. It is also a major nosocomial pathogen. The presence of highly-resistant subpopulation of cells termed "persisters" is proposed for higher drug resistance in E. faecalis biofilms. This study aimed to investigate the molecular mechanism behind E. faecalis biofilm persisters. Methods: Growth kinetics of E. faecalis biofilms was assessed in a time-dependent assay using colony forming unit (CFU) counting, crystal violet (CV) assay and Taqman PCR. The susceptibility of E. faecalis planktonic and biofilm cultures to chlorhexidine (CHX) was examined. E. faecalis proteins were extracted from planktonic cells, biofilms and the biofilms treated with CHX. Differentially expressed proteins were deduced by systems biology using proteomics and bioinformatics. Results: E. faecalis biofilms showed maximal biomass and stability at 72 h. They were highly resistant against CHX with reference to the planktonic cells. Oxidative defense system-associated proteins including alcohol dehydrogenase, peroxiredoxin and alkyl hydrogen peroxide reductase were up-regulated in the E. faecalis biofilm proteome compared to the planktonic proteome. E. faecalis biofilm exhibited higher capacity to produce quorum sensing molecules like pheromone cAD1 lipoprotein. CHX resistant E. faecalis persister cells possessed higher expression of antioxidant protein and thioredoxin which could contribute to the increased resistance. Conclusions: This study unraveled for the first time the different proteomics expression profiles of E. faeclias biofilm persister cells. This novel mechanism may explain the ability of E. faecalis to survive in root canals as a persistent colonizer (Supported by HKU Research Output Prize to LPS).