Objective To assess whether hospital profiles for public reporting and pay‐for‐performance, measured by the Agency for Healthcare Research and Quality (AHRQ) Patient Safety for Selected Indicators (PSI‐90) composite measure, were affected by using the recently developed harm‐based weights. Data Sources/Study Setting Retrospective analysis of 2012–2014 data from the Veterans Health Administration (VA). Study Design The AHRQ PSI software (v5.0) was applied to obtain the original volume‐based PSI‐90 scores for 132 acute‐care hospitals. We constructed a modified PSI‐90 using the harm‐based weights developed by AHRQ. We compared hospital profiles for public reporting and pay‐for‐performance between these two PSI‐90s and assessed patterns in these changes. Principal Findings The volume‐based and the harm‐based PSI‐90s were strongly correlated (r = 0.67, p < .0001). The use of the harm‐based PSI‐90 had a relatively small impact on public reporting (i.e., 5 percent hospitals changed categorization), but it had a much larger impact on pay‐for‐performance (e.g., 15 percent of hospitals would have faced different financial penalties under the Medicare Hospital‐Acquired Condition Reduction Program). Because of changes in weights of specific PSIs, hospital profile changes occurred systematically. Conclusions Use of the harm‐based weights in PSI‐90 has the potential to significantly change payments under pay‐for‐performance programs. Policy makers should carefully develop transition plans for guiding hospitals through changes in any quality metrics used for pay‐for‐performance.