Eleven children with acute encephalopathy associated with an influenza virus infection were treated during the 1997-1998 influenza season. Reverse transcription-polymerase chain reaction (RT-PCR) assay was used to detect the viral genome in peripheral blood and cerebrospinal fluid (CSF) samples. The results were compared with those of control influenza patients without neurological complications. Viral RNA was detected only in the peripheral blood mononuclear cells of one patient with influenza-virus-associated encephalopathy (1 of 9; 11%) and in the CSF of another patient (1 of 11;9%). RT-PCR was negative in the blood of all the controls, but the percentage of RT-PCR-positive samples in the two groups was not significantly different. Cytokines and soluble cytokine receptors in plasma and CSF were then quantified using an enzyme-linked immunosorbent assay. The CSF concentrations of soluble tumor necrosis factor receptor-1 were elevated in two patients and interleukin-6 (IL-6) was elevated in one patient with influenza-virus-associated encephalopathy. On the other hand, the plasma concentrations of IL-6 were elevated in four of nine patients. The number of encephalopathy patients who had elevated plasma concentrations of IL-6 100 pg/ml was significantly higher than that of controls (P= .01). In conclusion, the infrequent detection of the viral genome in the CSF and blood showed that direct invasion of the virus into the central nervous system was an uncommon event. Proinflammatory cytokines and soluble cytokine receptors may mediate the disease. The high plasma concentration of IL-6 could be an indicator of the progression to encephalopathy.