Six cases of amoebic encephalitis admitted to the National Institute of Neoplastic Diseases between the years 1994-2010 in Peru are reported. These cases were admitted for clinical suspicion of malignant primary brain tumor and one orbital-nasal sarcoma. All cases came from coastal regions; three were less than 24 years of age and four were male. The most common symptoms were headache and seizures. Three cases had more than one brain lesion. Stereotactic biopsy was performed in three patients and the differential pathological diagnosis in two cases was glioma of high and low grade. It was possible to confirm the diagnosis using molecular techniques in paraffin-embedded samples in three cases. All patients died within 15 days of admission to the institution. Amoebic encephalitis may be erroneously interpreted as a cerebral neoplasm, causing delay in the management of the infection.