Human herpesvirus-6B (HHV-6B) encephalitis can clinically manifest as hemorrhagic shock and encephalopathy syndrome (HSES), acute encephalopathy with biphasic seizures and late reduced diffusion (AESD), and acute necrotizing encephalopathy (ANE). To compare the underlying pathophysiology, we measured several biomarkers of interest in patients with these three different courses. Based on their clinical course and neuroimaging analysis, Cases 1, 2 and 3 were diagnosed as HSES, AESD, and ANE, respectively. HHV-6B was isolated from peripheral blood obtained during the acute phase in all three patients, and was detected in the cerebrospinal fluid of Cases 2 and 3. In Case 1, a marked increase in levels of several serum cytokines (IL-1β, IL-6, and IL-10) and chemokines (IL-8, MIG, MCP-1, and IP-10) was observed at disease onset. Subsequently, serum cytokine levels gradually became undetectable and chemokine levels stabilized by day 11 of illness. In Case 2, only two cytokines (IL-6 and IL-10) were slightly elevated at disease onset. In Case 3, the kinetics appeared to follow an up-and-down pattern. Additionally, in all three patients, TIMP-1 concentrations remained high during the observation period, and MMP-9 decreased quickly a few days after disease onset, and then returned to normal level.