The Waste Isolation Pilot Plant (WIPP) is being developed by the U.S. Department of Energy (DOE) for the geologic (deep underground) disposal of transuranic (TRU) waste. A Compliance Certification Application (CCA) of the WIPP for such disposal was submitted to the U.S. Environmental Protection Agency (EPA) in October 1996, and was approved by EPA in May 1998. In June 1998, two separate, but related, lawsuits were filed, one against DOE and one against EPA. On March 22, 1999, the court ruled in favor of DOE, and on March 26, 1999, DOE formally began disposal operations at the WIPP for non-mixed (non-hazardous) TRU waste. Before the WIPP can begin receiving mixed (hazardous) TRU waste, a permit from the State of New Mexico for hazardous waste disposal needs to be issued. It is anticipated that the State of New Mexico will issue a hazardous waste permit by November 1999. It is further anticipated that the EPA lawsuit will be resolved by July 1999. Congress (Public Law 102-579, Section 8(f)) requires the WIPP project to be recertified by the EPA at least as frequently as once every five years from the first receipt of TRU waste at the WIPP site. As part of the DOE's WIPP project recertification strategy, Sandia National Laboratories (SNL) has used systems analysis and performance assessment to prioritize its scientific and engineering research activities. Two 1998 analyses, the near-field systems analysis and the annual sensitivity analysis, are discussed here. Independently, the two analyses arrived at similar conclusions regarding important scientific activities associated with the WIPP. The use of these techniques for the recent funding allocations at SNL's WIPP project had several beneficial effects. It increased the level of acceptance among project scientists that management had fairly and credibly compared alternatives when making prioritization decisions. It improved the ability of SNL and its project sponsor, the Carlsbad Area Office of the DOE, to demonstrate the importance of ongoing scientific and engineering activities associated with the WIPP project. Finally, it provided objective documentation of the decision-making process for issues with an impact on safety at the WIPP, a critical topic for the general public and the regulatory agencies