Karnal bunt is difficult to identify in the field. Developing wheat kernels are randomly infected and usually only partially converted to the fungus, which is why KB is sometimes called partial bunt. Infection typically occurs in only a few seeds per head, and not all heads on a single plant are infected. Infected grain shows no symptoms until near maturity. Even then, the disease is difficult to detect in the field. The grain must be threshed and examined.

The diseased portion of kernels is dark in color and fishy smelling. The kernel usually remains whole, with only a part of the germ end converted into a black powdery spore mass, usually along the kernel groove. In extreme cases, the entire kernel is converted into spores. Examination must be done carefully, since three other diseases can be mistaken for KB: black point, common bunt, and dwarf bunt. Large, dark teliospores are diagnostic.

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