Two shallot (Allium cepavar.ascalonicumL.) cultivars, ‘Mikor’ and ‘Jermor’, were used to test a protocol forin vitrovirus elimination. Basal explants were prepared, surface sterilised, and placed onto a medium consisting of Murashige and Skoog (M & S) salts and vitamins with the addition of 3% sucrose, 1.0 mg/litre benzyladenine, 50 mg/litre ribavirin, and 0.8% agar. The explants underwent 5–6 days of continuous heat therapy: 4 h light at 35°C; 4 h dark at 31°C. When the shoots were 2–3 cm long they were excised, transferred to shoot inducing medium without ribavirin (the anti‐viral chemical), and grown under normal tissue culture conditions of 24°C under fluorescent lights with a photoperiod of 16 h. Finally, the plantlets were introduced to a bulb inducing medium (M & S salts and vitamins, 120 g/litre sucrose, 5 g/litre activated charcoal) for 2 monthsin vitrobefore being tested for onion yellow dwarf and shallot latent viruses by ELISA (enzyme‐linked immunosorbent assay) and transferred either to the glasshouse or into long‐term storage (6°C with a photoperiod of 16 h). Virus assays have confirmed that 60% of resulting ‘Jermor’ and 62.0% of ‘Mikor’ grownin vitroplants were free of shallow latent and onion yellow dwarf virus infections.