To detect an 18S ribosomal DNA fragment of Toxoplasma gondii Nested-PCR was used to detect an 18S ribosomal DNA fragment of Toxoplasma gondii in the CSF of 13 patients at 6 facilities in whom Toxoplasma meningoencephalitis had been suspected between January 2001 and Feburary 2005. Based on the diagnostic criteria of the CDC, all patients were treated with the anti-toxoplasmic chemotherapy based on the clinical diagnosis. Clinical improvement was observed in 11 patients, and the final diagnosis was toxoplasmosis, but the conditions of 2 patients deteriorated, and they were ultimately diagnosed with malignant lymphoma. Based on the results of the clinical diagnosis, we assessed the effectiveness of the nested-PCR method of examining the CSF for making the diagnosis of Toxoplasma meningoenephalitis. The results of the nested-PCR were positive in 8 of the 13 cases, and all 8 cases had been diagnosed with Toxoplasma encephalitis clinically. The results were negative in 5 of the 13 cases, but 3 of the 5 negative cases had been clinically diagnosed as toxoplasmosis, indicating that the test was false-negative in some cases (27.3%; 3/11). Toxoplasma meningoencephalitis is so difficult to diagnose that the development of the new, high-specificity diagnostic methods is being eagerly awaited.