We conducted a study to assess the characteristics, treatment and outcomes associated with Clostridium difficile associated diarrhea in a Veterans Affairs Medical Center. Fifty-eight consecutive individual cases of C. difficile infection in 2013 were observed within the Veterans Affairs New Jersey Health Care System (VA NJHCS). We molecularly typed all 58 individual strains and identified the associated characteristics, treatment and outcomes. Forty-four out of 58 specimens (76%) which were probed had characteristics of the epidemic strain BI/NAP1/027 making this virulent strain to be the predominate strain at the VA NJHCS. All C. difficile BI/NAP1/027 strains were resistant to fluoroquinolones and sensitive to fidaxomicin, metronidazole and vancomycin. Fidaxomicin had the most potent in vitro activity (MIC90 = 0.5 μg/ml) against the BI/NAP1/027 strain. Twenty-six of 44 patients (59%) with the virulent strain were from a long-term care facility (LTCF). Patients possessing the virulent strain from the LTCF had a mean APACHE II score of 14.1 and a predicted death rate of 21.9%. Two-third of patients were treated with metronidazole alone (mean APACHE II scores 9.6), and one-third required oral vancomycin and metronidazole (mean APACHE II scores 14.1). There were no C. difficile infection related deaths. C. difficile BI/NAP1/027, an epidemic strain, is the endemic strain at the VA NJHCS, but no increased mortality was seen with infection with this strain.