Tick-borne encephalitis (TBE) is a growing public health concern in central and 
northern European countries. Even though TBE is a notifiable disease in Croatia, 
there is a significant lack of information in regard to vector tick 
identification, distribution as well as TBE virus prevalence in ticks or 
animals. The aim of our study was to identify and to investigate the viral 
prevalence of TBE virus in ticks removed from red fox (Vulpes vulpes) carcasses 
hunted in endemic areas in northern Croatia and to gain a better insight in the 
role of wild ungulates, especially red deer (Cervus elaphus) in the maintenance 
of the TBE virus in the natural cycle. We identified 5 tick species (Ixodes 
ricinus, Ixodes hexagonus, Haemaphysalis punctata, Dermacentor reticulatus, 
Rhipicephalus sanguineus) removed from 40 red foxes. However, TBE virus was 
isolated only from adult I. ricinus and I. hexagonus ticks showing a viral 
prevalence (1.6%) similar to or higher than reported in endemic areas of other 
European countries. Furthermore, 2 positive spleen samples from 182 red deer 
(1.1%) were found. Croatian TBE virus isolates were genetically analyzed, and 
they were shown to be closely related, all belonging to the European TBE virus 
subgroup. However, on the basis of nucleotide and amino acid sequence analysis, 
2 clusters were identified. Our results show that further investigation is 
needed to understand the clustering of isolates and to identify the most common 
TBE virus reservoir hosts in Croatia. Sentinel surveys based on wild animal 
species would give a better insight in defining TBE virus-endemic and possible 
risk areas in Croatia.