Enterococcus faecalis is useful as a harmless fermentation organism and probiotic, but is also a common culprit of nosocomial infections. Clinical, food, commensal isolates were genotypically and phenotypically analyzed for the presence and expression of known virulence genes or factors under conditions in food (processing) (nitrite, osmotic, acid, heat, high pressure), and during gut transit (BHI broth, bile salts, intestinal epithelial cells, mouse model) by RT-PCR and Northern (dot) blot analysis. Origin of isolation did not correlate with the number or types of virulence gene, and environmental stresses differentially impact E. faecalis stress and virulence gene expression. Preventative measures for applications of E. faecalis strains include absence of fsrB and agg and minimizing stress induced pre-conditioning for virulence in food processing.