Patient Safety Indicators (PSIs), developed by the Agency for Healthcare Research and Quality (AHRQ), are administrative data-based indicators that identify potential in-hospital patient safety events. This study developed and tested methods for (1) applying PSIs to Department of Veterans Affairs (VA) discharge data, and (2) comparing VA with non-VA PSI rates. VA inpatient data file structure and elements were modified in order to apply PSIs to VA data; further modifications were required to compare VA and non-VA PSI rates. We found that key measures, including demographics, clinical elements, and length of stay, as well as the PSI rates themselves, are sensitive even to minor data modifications. This paper demonstrates both the adaptation of a database for use with the PSIs, and the sensitivity of PSI rates to small differences in database characteristics. The paper shows how differences in data sources might affect comparisons of event rates across health care systems.