Porcine endogenous retrovirus (PERV) is considered the major biosafety issue in xenotransplantation. Several techniques have been employed for the analysis of the PERV status in the animal donor and for the assessment of PERV transmission/infection in the xenograft recipient. In this chapter, methods to assess the expression of PERV and the potential for PERV transmission from a donor animal are described in addition to the identification of relevant loci within the porcine genome.PERV detection can be carried out using several techniques of which quantitative polymerase chain reaction (PCR) and RT-PCR are the most sensitive. However, other procedures can be employed such as detection of reverse transcriptase activity (i.e. viral replication) in the sample or immunostaining of the infected cells using an anti-PERV antibody. The PERV transmission assay has been described to identify the transmission phenotype of the pig donor, and subsequent risk from a donor. This assay can, therefore, direct the selection of the most suitable animal. Finally, it is important to determine the presence of critical PERV loci involved in transmission in the pig genome and compare between different animals. One of the methods for the analysis of these PERV integration sites is described.