We have reported that there are distinct domains in Interferon-alpha (IFNalpha) molecule mediating immune and opioid-like effects respectively. And the opioid effect of IFNalpha is mediated by mu opioid receptor. We report here the structural basis of fever induced by recombinant human IFNalpha. Two kinds of IFNalpha mutants were obtained and used to investigate the structural basis of fever of IFNalpha, which are 129Ser-IFNalpha and 38Leu-IFNalpha. The antiviral activity of 129Ser-IFNalpha almost disappeared, but there still retained the strong analgesic activity. The antiviral activity of 38Leu-IFNalpha remained, but the analgesic activity disappeared completely. It showed that IFNalpha and 129Ser-IFNalpha decreased cAMP production, induced the fever, and stimulated PGE2 to release from the hypothalamus slices, which could be blocked by naloxone, but 38Leu-IFNalpha failed. It is the first demonstration that fever induced by IFNalpha is mediated by opioid domain of IFNalpha interacting with opioid receptor. It is inferred that high-activity and low side-effect IFNalpha or other cytokines could be obtained after being changed the motifs in the tertiary structure.