This three-year study compared the use of ELISA and RT-PCR for identifying Prunus necrotic ringspot virus (PNRSV) and prune dwarf virus (PDV) on 175 leaf samples taken from trees maintained as a budwood repository for almond growers. The primers used for RT-PCR were based on DNA sequences that code for coat protein, and both viruses could be detected in the same reaction. For PNRSV, both ELISA and RT-PCR produced similar results, although RT-PCR was more consistent, and had the added advantage that plant material could be tested at any time throughout the growing season. For PDV, virus particles were not detected by ELISA, but were detected in low titre using a nested PCR technique. RT-PCR is used routinely now to index progeny developed each year by the Australian almond improvement program in place of both graft incompatibility using woody indicator species and ELISA.