BACKGROUND: Pathogens transmitted by ticks cause human disease on a greater scale than any other vector-borne infections in Europe, and have increased dramatically over the past 2-3 decades. Reliable records of tick-borne encephalitis (TBE) since 1970 show an especially sharp upsurge in cases in Eastern Europe coincident with the end of Soviet rule, including the three Baltic countries, Estonia, Latvia and Lithuania, where national incidence increased from 1992 to 1993 by 64, 175 and 1,065%, respectively. At the county level within each country, however, the timing and degree of increase showed marked heterogeneity. Climate has also changed over this period, prompting an almost universal assumption of causality. For the first time, we analyse climate and TBE epidemiology at sufficiently fine spatial and temporal resolution to question this assumption. METHODOLOGY/PRINCIPAL FINDING: Detailed analysis of instrumental records of climate has revealed a significant step increase in spring-time daily maximum temperatures in 1989. The seasonal timing and precise level of this warming were indeed such as could promote the transmission of TBE virus between larval and nymphal ticks co-feeding on rodents. These changes in climate, however, are virtually uniform across the Baltic region and cannot therefore explain the marked spatio-temporal heterogeneity in TBE epidemiology. CONCLUSIONS/SIGNIFICANCE: Instead, it is proposed that climate is just one of many different types of factors, many arising from the socio-economic transition associated with the end of Soviet rule, that have acted synergistically to increase both the abundance of infected ticks and the exposure of humans to these ticks. Understanding the precise differential contribution of each factor as a cause of the observed epidemiological heterogeneity will help direct control strategies.