In addition to mycotic infections, there are two other kinds of fungal disease: (1) mycotoxicoses, caused by ingested toxins, and (2) allergies to fungal spores. The best-known mycotoxicosis occurs after eating Amanita mushrooms. These fungi produce five toxins, two of which amanitin and phalloidin are among the most potent hepatotoxins. The toxicity of amanitin is based on its ability to inhibit cellular RNA polymerase, which prevents mRNA synthesis. Another mycotoxicosis, ergotism, is caused by the mold Claviceps purpurea, which infects grains and produces alkaloids (e.g., ergotamine and lysergic acid diethylamide [LSD]) that cause pronounced vascular and neurologic effects.

Other ingested toxins, aflatoxins, are coumarin derivatives produced by Aspergillus flavus that cause liver damage and tumors in animals and are suspected of causing hepatic carcinoma in humans. Aflatoxins are ingested with spoiled grains and peanuts and are metabolized by the liver to the epoxide, a potent carcinogen. Aflatoxin B1 induces a mutation in the p53 tumor suppressor gene, leading to a loss of p53 protein and a consequent loss of growth control in the hepatocyte.

Allergies to fungal spores, particularly those of Aspergillus, are manifested primarily by an asthmatic reaction (rapid bronchoconstriction mediated by IgE), eosinophilia, and a "wheal and flare" skin test reaction. These clinical findings are caused by an immediate hypersensitivity response to the fungal spores.