Aspergillus and Candida are the most common secondary fungal infections, causing chronic diarrhea with severe ulceration of the intestinal wall. These fungi are of particular importance when animals are being treated for long periods with antibiotics which may destroy the normal protective bacteria in the gut leaving the way open for the fungi to become established.

Fungi which can cause primary infections include Pythium, Histoplasma, Zygomycetes, and Mucoraceae families. They are more commonly seen in larger breeds of dogs which may reflect greater access to swampy fungal infected water, considered to be a major source of infection. These fungi tend to produce weight loss, diarrhea and vomiting which resist normal treatments. The gut becomes thickened and the surrounding glands (lymph nodes) may become very swollen.

Diagnosis can be difficult and relies upon identifying the fungi in biopsy of the gut and lymph nodes. The condition can be easily mistaken for cancer by signs and appearance.

Treatment is also very difficult and requires both surgical removal of the effected gut and prolonged antifungal drugs such as Ketoconazole or Amphotericin B