The importance and frequency of invasive fungal infections in different organs, including the gastrointestinal tract, has increased due to excessive use of aggressive immunosuppressive and immunomodulatory drugs in malignant diseases and organ transplantations as well as increased infections with the human immunodeficiency virus (HIV). Fungal infections in the small intestine or colon are usually part of a disseminated disease process and reach these organs through the bloodstream. Two of the patients were infants 10 and 15 days of age, while one was 23 years old. Patients presented with abdominal pain, intestinal obstruction, and rectal bleeding. Hirchsprung disease was suspected in the two infants. In the adult patient, the diagnosis was unclear. Mucormycosis was diagnosed in two out of three cases. It is imperative for clinicians to consider invasive mycosis in the differential diagnosis in patients of all ages with treatment-resistant severe abdominal pain, diarrhea and fever.