Abstract Commercially distributed garlic (Allium sativum) seed cloves from six states of the United States and mainland China were surveyed for the presence of fungi recorded as pathogenic to garlic in the literature. Aspergillus niger, A. ochraceus, Botrytis porri, Embellisia allii, Fusarium oxysporum f. sp. cepae, F. proliferatum and Penicillium hirsutum, were each recovered from one or more of these commercial sources, as was F. verticillioides, not previously reported as pathogenic to garlic, but here demonstrated to be a pathogen. Seed garlic distributed from public germplasm collections may also contain fungal pathogens: E. allii, F. oxysporum f. sp. cepae and/or F. proliferatum caused severe losses in 2002–2003 and 2005–2006 during germplasm regeneration and storage for the National Plant Germplasm System in Pullman, Washington. Use of fludioxonil, thiophanate methyl and/or benomyl (the latter withdrawn from the market, but used here as a standard) at label rates against E. allii and Fusarium species promoted plant health, but not when infections were located deep within tissues nor under some situations involving high disease pressure.