Objective To understand the effects of mRNA assay for enterovirus in cerebrospinal fluid (CSF) of patients by using reverse transcription polymerase chain reaction (RT-PCR) on clinical diagnosis and therapy of viral encephalitis. Methods RT-PCR with one pair of picornaviridae-specific primer (PSP) against the conserved 5'noncoding region of enterovirus (EV) was employed to investigate enterovirus RNA in CSF of 43 patients who were diagnosed as viral encephalitis by their clinical features.The patients' symptoms, abnormal signs and laboratory evaluation including routine examinations of CSF,CSF biochemistry, antibodies to other virus in CSF, cranial computed tomography (CT), cranial magnetic resonance imaging (MRI) and electroencephalogram (EEG) were observed and statistically analyzed by Student's tests. Results By the CSF EV RT-PCR, 18 out of 43 patients, most of them male, were tested to be EV positive (41.9%), and their symptoms and signs were not significantly different from that of EV negative. The albumen and cell content in CSF of the patients of EV positive was higher than patients of negative. Sometimes antibodies to other virus could be found in serum of EV positive patients.Conclusion Viral encephalitis owing to enterovirus has higher morbidity and sometimes goes with other virus infection. The results of EV RT-PCR are not always consistent with that of serum assay. The result of EV RT-PCR could be used to guide clinical diagnosis and treatment.