A method for the detection of Onion yellow dwarf virus (OYDV) and Leek yellow stripe virus (LYSV), the two most prevalent garlic potyviruses, has been developed that combines IC-RT-PCR/RT-PCR with the use of TaqMan probes. Comparisons with ELISA results obtained with identical OYDV and LYSV infected samples showed sensitivity in detecting these viruses increased up to 10(6)-fold. OYDV and LYSV were detected using different fluorochromes in the probe, thus allowing unequivocal diagnosis for each of them. The polyvalence of the designed virus-specific primers and probes was shown through their application to the detection of three isolates from very different geographical areas and from different hosts. A second version of the method avoids the need for an immunocapture step through the performance of a TaqMan RT-PCR assay directly on extracts of garlic cloves. This modification on the proposed basic method allows the analysis of bulb samples in 3-4h but did not give reproducible results with leaves. Both versions of the new diagnostic method bear great potential for their implementation in virus-free certification schemes in garlic, a vegetatively propagated crop for which such a certification is critical for a high-quality product.