The full genome sequences of three tick-borne encephalitis virus strains, two isolated from Ixodes ricinus ticks and one from the brain of a bank vole, Myodes glareolus, originating from the Slovak Republic were determined. Nucleotide sequences were found to be very similar (>99.5 % nt-identity) with only one distinct amino acid (aa) difference to each other. They all shared 30 aa-changes when compared to type strain Neudoerfl, isolated in neighboring Austria. An internal poly(A)-stretch similar to that of strain Neudoerfl was found only in TBEV strain 114 from a tick. Despite this heterogeneity in the 3'-NCR, the high level of sequence identity was striking, indicating a low rate of nucleotide substitutions of TBEV strains in Slovakia and no obvious relation to the host species.