Tick-borne encephalitis (TBE) incidence increased markedly in the Baltics and Slovenia in the early 1990s, but then declined again in some places. Our analyses of temporal and spatial data on TBE incidence and vaccination revealed that over 1970-2005 up-take of vaccination varied in both time and space according to incidence, i.e. was apparently responsive to perceived risk. Since 1999, however, decreases in incidence in many counties within each country have far exceeded vaccination rates or immunity through natural exposure, and in Latvia and Lithuania these changes are correlated with previous incidence. Survey data on human activities in Latvia revealed that people in socio-economic groups whose behaviour put them at highest risk of exposure to ticks in forests, including people with lower education and lowest incomes, are least likely to be vaccinated. We conclude that risk avoidance through changing human behaviour has driven incidence-dependent decreases in TBE infection, but targeted vaccination campaigns could provide more secure protection.