Hypocotyl rot affects the stem of the plant between the cotyledons and the roots (the hypocotyl). The fungal organism, Rhizoctonia, is very common in most soils. Hypocotyl rot affects isolated plants, as opposed to Rhizoctonia bare patch which occurs in patches. Seedlings are infected during emergence and die rapidly, reducing emergence. Any surviving plants will be stunted and prone to other problems such as collar rot.
Hypocotyl rot is worse in crops following the pasture phase in a rotation, and is also promoted by early sowing. Affected plants are characterised by red-brown lesions on the hypocotyl or tap root.