Deer fascioloidosis is a serious and potentially fatal disease caused by the non-native trematode Fascioloides magna. Infections of red deer with F. magna in Croatia have been reported for the first time in 2000 in the Baranja region. Subsequently, the disease spread throughout the Eastern parts of the country, involving all 3 deer species (red, roe, and fallow) and mouflons. Within the disease control programme (DCP), livers from all shot deer were thoroughly analysed and all detected trematodes and gross lesions were counted and categorized. Prevalence of positive animals, in this study for Spačva region, in the period ranging from 2007 to 2012 was 36.42% (46.39% when fawns are not considered). Epidemiological analysis was applied to evaluate risk factors and disease patterns at the population level with the aim to understand factors with negative influence on therapeutic effect. Each demographic variable was tested at the seasonal, individual and location level. Model for pathological lesions suggested that the likelihood of lesions was dependent on age (p = 0.003). We did not find any locality or sex related significant differences. Finally, environmental characteristics and migratory patterns were analysed using Geographic Information System (GIS) and showed that Spačva region represents an epidemiological unit for red deer fascioloidosis.