The morbidity of tick-borne encephalitis (TBE) varies yearly by as much as 10-fold among the people of Western Siberia. This long-term variation is dependent on many factors such as the density of the tick populations, the prevalence of TBE virus (TBEV) among sub-adult ticks, the yearly virulence of the TBEV, and prophylactic measures. Here we highlight the role of small mammal hosts in the circulation of TBEV through the ecosystem. Refining classical models of non-viremic horizontal transmission, we emphasize the recently understood fact that the physiological and immunological status of the small mammal hosts affects the tick and virus-host interactions. In addition to its theoretical interest, our approach may lead to some practical improvements in the precision of epidemiological forecasts and perhaps in forestalling the severity of outbreaks of TBE, or, at least, in forewarning medical authorities and the general public of impending TBE outbreaks.