Tick-borne encephalitis (TBE) is a severe problem in Lithuania, indicated by the 171 to 645 serologically confirmed cases that occurred each year between 1993 and 1999. In the present report, the first isolation and partial genetic analysis of a Lithuanian TBE virus (TBEV) strain isolated from a patient's serum sample is described. The patient was bitten by a tick while visiting the Lazdijai district (Veisiejai forest) in the southernmost part of Lithuania, a geographical area where Ixodes ricinus but not Ixodes persulcatus ticks are known to be present. The E protein-encoding viral gene sequence (nt 74-1273) recovered from the TBEV isolate showed the closest similarity to previously characterized European strains of the Western TBEV subtype, including the prototype TBEV strain Neudoerfl and those from neighbouring Latvia. Accordingly, the Lithuanian isolate was placed within the Western genetic lineage of TBEV in phylogenetic trees.