Tick-borne encephalitis virus (TBEV) and Louping ill virus (LIV) are viruses in the Mammalian tick-borne virus group/genus Flavivirus, causing central nervous system disease. Greek goat encephalitis virus (GGEV), which was isolated from the brain of a newborn goat with neurological symptoms, is currently classified in the TBEV group. The vector of GGEV has not yet been specifically identified but is considered likely to be Ixodes ricinus. A total of 3,144 Ixodidae ticks collected during 2003-2006 from goats and sheep in rural areas of Northern Greece were tested by reverse transcription-polymerase chain reaction (RT-PCR) for the presence of TBEV-specific RNA. Two pools of I. ricinus ticks were shown to be RNA-positive. Sequence analysis showed that the virus was GGEV. The RNA-positive ticks were detected in regions where high prevalence of TBE antibodies in humans was present. Prevalence in ticks varied according to year, season, and geographic region. TBEV is not endemic in Greece, and most probably the seroprevalence of TBE antibodies in humans is due to cross-reactivity to GGEV.