BACKGROUND: West Nile virus (WNV) emerged in central Macedonia, northern Greece, in 2010. The aim of the study was to test Culex mosquitoes for genetic detection of WNV and other flaviviruses, and to check whether the detection of WNV in mosquitoes was correlated with the occurrence of human WNV cases.METHODS: During 2013, 25 780 Culex spp. mosquitoes were collected from central Macedonia, grouped into 295 pools, according to collection site and date, and tested for the presence of flavivirus RNA.RESULTS: Thirteen (4.4%) pools were flavivirus-positive. WNV lineage 2 was detected in nine (3.1%) pools, and insect-specific flaviviruses (ISFV) in four (1.4%). Three ISFV nucleotide sequences were 98% identical to Culex theileri flavivirus, previously detected in the Iberian peninsula, while the fourth sequence differed by >25% from all known flaviviruses. In most units of central Macedonia WNV detection in mosquitoes preceded the occurrence of human cases by approximately one month.CONCLUSIONS: Detection of WNV lineage 2 in mosquitoes for a fourth consecutive year suggests that the virus is established in Greece. Entomological surveillance provides an early warning system for the circulation of the virus. The detection of Culex theileri flavivirus extends the known range of this virus.