Delays in research on emerging infections could deprive the public of appropriate therapies. This report describes challenges encountered in implementing two multicenter protocols of West Nile virus (WNV) infections in the United States during 2003. Protocol development times, federal regulatory approvals, and local Institutional Review Boards (IRB) approvals were compiled. Twenty eight institutions participated in a natural history study and 27 in a therapeutic trial of WNV developed through the National Institute of Allergy and Infectious Disease Collaborative Antiviral Study Group (CASG). The CASG compiled protocol development times, federal regulatory approvals, and local IRB approvals. Additional information on the local IRB process was obtained by survey of the investigators. Because of the lengthy development and approval process, protocols were distributed after the start of the epidemic season, most sites were unable to enroll subjects at the peak of the season, and a number of sites lacked IRB approval at the end of the season.