We report a case of extensive pseudofungi in the pericolic lymph nodes. A 45-year-old man presented with lower abdominal discomfort, and large solid and cystic masses were discovered in the pelvic cavity by computed tomography. Debulking of the masses (by means of a Hartmann operation) was performed under the clinical impression of a pelvic sarcoma, and histologically the masses demonstrated features of a malignant gastrointestinal stromal tumor. All pericolic lymph nodes demonstrated multiple septate hyphae-like structures with pigmentation, particularly in the subcapsular sinuses. These structures showed positive staining with periodic acid-Schiff, but Gomori methenamine silver staining was negative. The structures appeared to be composed of iron, phosphorus, and calcium by Perls iron and von Kossa stains and revealed deposition of electron-dense granules on electron microscopic examination. Energy-dispersive radiographic micro-analysis showed the structures to contain phosphorus, sulfur, potassium, calcium, and iron. Pseudofungi can be misinterpreted as true fungi with septate hyphae; therefore, a careful morphologic examination with appropriate special stains is mandatory.