Yields in large‐scale ‘continuous’ cultivation of H. tuberosus (Jerusalem artichoke) can be greatly reduced by Sclerotinia sclerotiorum, which causes a basal stem and tuber rot. In 34 varieties/lines of H. tuberosus from European, Russian and Canadian breeding programmes, responses to the pathogen varied from field resistance to 34% stem rot, cultivars Nahodka and Columbia showing c. 25% stem rot after three seasons of cultivation on the same site. Attempts to develop an in‐vitro selection for S. sclerotiorum resistance based on culture of H. tuberosus nodes on media precolonized with Sclerotina were unsuccessful. There was a strong positive correlation between capacity of nodes to grow in vitro on calcium‐free medium and field resistance. Somaclones of'Nahodka’ selected on the latter basis showed no field infection when grown on land that was heavily contaminated with the pathogen, and they were resistant to artificial inoculation with the pathogen.