The opportunistic pathogens, Acanthamoeba and Balamuthia, are the causative agents of the fatal central nervous system (CNS) infection granulomatous amoebic encephalitis. We report an infection of Acanthamoeba in an HIV+ individual. In the present case, multiple lesions were observed in the skin, brain, lung, liver, and bone. A polymerase chain reaction (PCR) assay specific for Acanthamoeba was positive on tissue from a brain biopsy that had been embedded in paraffin. This report demonstrates the need for the consideration of Acanthamoeba infections in HIV+ individuals with skin lesions and multiple lesions throughout the body with CNS involvement. The results of the present study demonstrate that opportunistic amoebic infections can be diagnosed by PCR from paraffin-embedded biopsy material.