Federal research regulations require participants to be informed about whether medical care or compensation for injury is available in more than minimal risk studies and prohibit language in informed consent documents that waives, or appears to waive, legal rights. The objectives of this study were to compare data collected in 2000 and 2012 to identify significant changes in types of institutional compensation policies at U.S. research institutions, and assess the relationship between institutional characteristics and different types of policies. We found that research-related injury compensation policies did not change substantially during the time period. A significant percentage of policies contain language that can be reasonably interpreted as waiving, or appearing to waive, legal rights. Level of funding, public vs. private status, and institutional involvement in clinical research were associated with different types of policies. The lack of substantial change in compensation policies supports arguments for a national policy.