Selection of a pre-operative hand antisepsis agent has not been studied in relation to surgical site infection (SSI) culture data. In our hospital, we introduced an alcohol-based hand rub (ABR) in 2012 as an alternative to traditional aqueous surgical scrubs (TSS). It was the goal of this study to review any effect of this implementation on SSI pathogen characteristics. In addition, we sought to compare our SSI culture data with available National Healthcare Safety Network (NHSN) data. We hypothesized that SSI pathogens and resistant isolates are affected by surgical hand antisepsis technique.Data collected prospectively between 2007 and 2014 were retrospectively analyzed for two time periods at the Veterans Affairs Boston Healthcare System (VABHS): Before ABR implementation (TSS group) and after (ABR group). Pathogen distribution and pathogenic isolate resistance profiles were compared for TSS and ABR, and similar comparisons, along with procedure-associated SSI comparisons, were made between VABHS and NHSN. All VABHS data were interpreted and categorized according to NHSN definitions.Compared with TSS (n = 4,051), ABR (n = 2,293) had a greater rate of Staphylococcus aureus (42.6% vs. 38.0%), Escherichia coli (12.8% vs. 9.9%), Pseudomonas aeruginosa (8.5% vs. 2.8%), and Enterobacter spp. (10.6% vs. 2.8%), and a lower rate of Klebsiella pneumoniae/K. oxytoca (4.3% vs. 8.5%) cultured from superficial and deep SSIs (p < 0.05). Of the S. aureus isolates, 35.0% and 44.4% were resistant to oxacillin/methicillin (MRSA) in ABR and TSS, respectively (p = 0.06). Looking at all SSIs, coagulase-negative staphylococci and K. pneumoniae/K. oxytoca at VABHS (4.0% and 10.4%, respectively) accounted for the biggest difference from NHSN (11.7% and 4.0%, respectively). Aside from MRSA, where there was no difference between VABHS and NHSN (42.9% vs. 43.7%, respectively; p = 0.87), statistically significant (p < 0.05) differences were observed among multi-drug-resistant K. pneumoniae/K. oxytoca (0% vs. 6.8%, respectively) and Escherichia coli (10.0% vs. 1.6%, respectively), as well as among extended-spectrum cephalosporin-resistant K. pneumoniae/K. oxytoca (4.8% vs. 13.2%, respectively) and Enterobacter (58.3% vs. 27.7%, respectively). VABHS had a greater proportion of SSIs in abdominal and vascular cases than did NHSN (48.6% vs. 22.5% and 13.2% vs. 1.5%, respectively). Overall, these differences were significant (p < 0.05).The TSS and ABR groups differed in the distribution of pathogens recovered. Those differences, along with SSI pathogen distribution, pathogenic isolate resistance profiles, and procedure-associated SSIs between VABHS and NHSN, warrant further investigation.