The Waste Isolation Pilot Plant (WIPP) in southeastern New Mexico has been developed by the U.S. Department of Energy (DOE) for the deep underground disposal of transuranic (TRU) waste. In October 1996, the DOE submitted the Compliance Certification Application (CCA) to the EPA. After extensive review, the CCA was certified in May 1998 signifying that the WIPP complied with disposal regulations. The first shipment of waste arrived at the site in March 1999. As part of the management of the WIPP, DOE is required to submit a Compliance Recertification Application (CRA) every five years, the first of which is due to the EPA in 2004. The CRA takes into account any information or conditions that have changed since the original certification decision. To support the CRA, the DOE is conducting a new performance assessment (PA). PA consists of a linked series of models and computer codes to make probabilistic assessments of the possible future states of the repository and the resulting radionuclide releases. Sandia National Laboratories, as the Scientific Advisor to the DOE, designs and runs the PA calculations. This presentation covers the transport calculations as part of the PA that determine the mobilization and migration of radioisotopes throughout the repository, shaft system, Salado formation, and possible human intrusion boreholes. More specifically, it addresses the conceptualization, numerics, methodology, and analysis of nuclide transport using the computer code NUTS (NUclide Transport System) and its role in the CRA PA calculations.